| --- |
| 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. |
