| | --- |
| | license: gpl-3.0 |
| | tags: |
| | - biology |
| | pretty_name: ProtHGT Knowledge Graph Data & Pretrained Checkpoints |
| | --- |
| | |
| | # ProtHGT Knowledge Graph Data & Pretrained Checkpoints |
| | This repository provides the **knowledge graph (KG) `.pt` files** and **pretrained model checkpoints** used in **ProtHGT: Heterogeneous Graph Transformers for Automated Protein Function Prediction Using Biological Knowledge Graphs and Language Models**. |
| | - **Code (training & prediction)**: https://github.com/HUBioDataLab/ProtHGT |
| |
|
| | --- |
| |
|
| | ## What’s Inside |
| |
|
| | ### data/ |
| | PyTorch Geometric-compatible KG files: |
| | - Full KG file (e.g., `prothgt-kg.pt`) |
| | - Train/validation/test splits (e.g., `prothgt-*-graph.pt`) |
| | - Alternative KG versions under `alternative_protein_embeddings/` (e.g., `esm2/`, `prott5/`), where the protein node features differ by embedding type. |
| |
|
| | **Available Files** |
| | ``` |
| | ├── prothgt-kg.pt # The default full knowledge graph containing TAPE embeddings as the initial protein representations. |
| | ├── prothgt-train-graph.pt # Training set (80% of the default full KG). |
| | ├── prothgt-val-graph.pt # Validation set (10% of the default full KG). |
| | ├── prothgt-test-graph.pt # Test set (10% of the default full KG). |
| | └── alternative_protein_embeddings/ # Contains alternative KGs with different protein representations. |
| | ├──apaac/ |
| | │ └── ... |
| | ├──esm2/ |
| | │ └── ... |
| | └──prott5/ |
| | └── ... |
| | ``` |
| |
|
| |
|
| | ### models/ |
| | Pretrained ProtHGT models (`.pt`). Models are provided: |
| | - per GO sub-ontology (e.g., Molecular Function / Biological Process / Cellular Component) |
| | - per protein embedding type (default vs `esm2` / `prott5` / etc.) |
| |
|
| | **Important:** Use a model checkpoint that matches the KG embedding variant you are using. |
| |
|
| | **Available Files** |
| | ``` |
| | ├── prothgt-model-molecular-function.pt # Pretrained ProtHGT checkpoint for Molecular Function (default/TAPE-based KG). |
| | ├── prothgt-model-biological-process.pt # Pretrained ProtHGT checkpoint for Biological Process (default/TAPE-based KG). |
| | ├── prothgt-model-cellular-component.pt # Pretrained ProtHGT checkpoint for Cellular Component (default/TAPE-based KG). |
| | └── alternative_protein_embeddings/ # Models trained with alternative protein representations. |
| | ├── esm2/ |
| | │ └── ... |
| | └── prott5/ |
| | └── ... |
| | ``` |
| |
|
| | --- |
| |
|
| | ### How to Use (Training & Prediction) |
| | To train or run inference, follow the instructions in the GitHub repository: https://github.com/HUBioDataLab/ProtHGT |
| |
|
| | Key scripts: |
| | - `train.py` — trains ProtHGT using the provided KG splits |
| | - `predict.py` — runs inference using pretrained checkpoints |
| |
|
| | --- |
| |
|
| | ### Citation |
| | Please refer to our preprint for more information. If you use the ProtHGT method or the datasets provided in this repository, please cite this paper: |
| | Ulusoy, E., & Dogan, T. (2025). ProtHGT: Heterogeneous Graph Transformers for Automated Protein Function Prediction Using Biological Knowledge Graphs and Language Models (p. 2025.04.19.649272). bioRxiv. [Link](https://doi.org/10.1101/2025.04.19.649272) |
| |
|
| | --- |
| |
|
| | ### Licensing |
| | Copyright (C) 2025 HUBioDataLab |
| |
|
| | This dataset is released under GPL-3.0. |
