junxia97 / awesome-pretrain-on-moleculesView external linksLinks
[IJCAI 2023 survey track]A curated list of resources for chemical pre-trained models
☆536Jun 17, 2023Updated 2 years ago
Alternatives and similar repositories for awesome-pretrain-on-molecules
Users that are interested in awesome-pretrain-on-molecules are comparing it to the libraries listed below
Sorting:
- [ICLR 2023] "Mole-BERT: Rethinking Pre-training Graph Neural Networks for Molecules"☆129Jun 9, 2023Updated 2 years ago
- Pre-training Molecular Graph Representation with 3D Geometry, ICLR'22 (https://openreview.net/forum?id=xQUe1pOKPam)☆210Sep 20, 2022Updated 3 years ago
- Official Repository for the Uni-Mol Series Methods☆1,054May 29, 2025Updated 8 months ago
- [ICLR 2023] One Transformer Can Understand Both 2D & 3D Molecular Data (official implementation)☆219Mar 31, 2023Updated 2 years ago
- ☆283Updated this week
- List of Molecular and Material design using Generative AI and Deep Learning☆916Jan 27, 2026Updated 2 weeks ago
- Multi-modal Molecule Structure-text Model for Text-based Editing and Retrieval, Nat Mach Intell 2023 (https://www.nature.com/articles/s42…☆250Jun 27, 2025Updated 7 months ago
- Strategies for Pre-training Graph Neural Networks☆1,049Jul 29, 2023Updated 2 years ago
- LLM for Drug Editing, ICLR 2024☆156May 28, 2024Updated last year
- Geom3D: Geometric Modeling on 3D Structures, NeurIPS 2023☆132Jun 5, 2024Updated last year
- This is a Pytorch implementation of the paper: Self-Supervised Graph Transformer on Large-Scale Molecular Data☆383Jun 24, 2025Updated 7 months ago
- Official implementation of pre-training via denoising for TorchMD-NET☆99Mar 2, 2023Updated 2 years ago
- A powerful and flexible machine learning platform for drug discovery☆1,566Aug 12, 2024Updated last year
- GEOM: Energy-annotated molecular conformations☆240Apr 24, 2022Updated 3 years ago
- Implementation of MolCLR: "Molecular Contrastive Learning of Representations via Graph Neural Networks" in PyG.☆315Nov 4, 2023Updated 2 years ago
- Hierarchical Generation of Molecular Graphs using Structural Motifs☆424Jun 28, 2022Updated 3 years ago
- Making self-supervised learning work on molecules by using their 3D geometry to pre-train GNNs. Implemented in DGL and Pytorch Geometric.☆172Oct 8, 2023Updated 2 years ago
- Implementation of MoLeR: a generative model of molecular graphs which supports scaffold-constrained generation☆317Jan 4, 2024Updated 2 years ago
- [ICLR 2024] Mol-Instructions: A Large-Scale Biomolecular Instruction Dataset for Large Language Models☆292Oct 28, 2024Updated last year
- Code and data for the Nature Machine Intelligence paper "Knowledge graph-enhanced molecular contrastive learning with functional prompt".☆136Mar 18, 2024Updated last year
- Molecular Sets (MOSES): A Benchmarking Platform for Molecular Generation Models☆950Jul 8, 2024Updated last year
- [ICLR 2024] Domain-Agnostic Molecular Generation with Chemical Feedback☆186Dec 17, 2024Updated last year
- Therapeutics Commons (TDC): Multimodal Foundation for Therapeutic Science☆1,205Jul 13, 2025Updated 7 months ago
- [ICLR 2024] MARCEL: Machine Learning over Molecular Conformer Ensembles☆44Jun 14, 2023Updated 2 years ago
- Message Passing Neural Networks for Molecule Property Prediction☆2,262Feb 3, 2026Updated last week
- Repository for MolFormer☆373Sep 17, 2025Updated 4 months ago
- MolRep: A Deep Representation Learning Library for Molecular Property Prediction☆129Sep 17, 2024Updated last year
- Original implementation of the paper "SMILES Transformer: Pre-trained Molecular Fingerprint for Low Data Drug Discovery" by Shion Honda e…☆352Dec 22, 2022Updated 3 years ago
- Official implementation of NeurIPS'21 paper"Motif-based Graph Self-Supervised Learning for Molecular Property Prediction"☆127Aug 18, 2023Updated 2 years ago
- bert-loves-chemistry: a repository of HuggingFace models applied on chemical SMILES data for drug design, chemical modelling, etc.☆486Oct 27, 2024Updated last year
- [WWW 2022] "SimGRACE: A Simple Framework for Graph Contrastive Learning without Data Augmentation"☆81Jun 13, 2022Updated 3 years ago
- Associated Repository for "Translation between Molecules and Natural Language"☆192Sep 15, 2023Updated 2 years ago
- Benchmarks for generative chemistry☆495Feb 11, 2024Updated 2 years ago
- Awesome papers related to generative molecular modeling and design.☆338Jul 20, 2025Updated 6 months ago
- ATOM3D: tasks on molecules in three dimensions☆318Mar 2, 2023Updated 2 years ago
- Papers about pretraining and self-supervised learning on Graph Neural Networks (GNN).☆1,711Feb 2, 2024Updated 2 years ago
- A Deep Learning Toolkit for DTI, Drug Property, PPI, DDI, Protein Function Prediction (Bioinformatics)☆1,130Jun 10, 2024Updated last year
- ☆333Mar 24, 2024Updated last year
- A tool for evaluating the predictive performance on activity cliff compounds of machine learning models☆205Feb 15, 2025Updated last year