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--- |
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license: gpl-3.0 |
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tags: |
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- biology |
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pretty_name: ProtHGT Knowledge Graph Data & Pretrained Checkpoints |
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--- |
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# ProtHGT Knowledge Graph Data & Pretrained Checkpoints |
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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**. |
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- **Code (training & prediction)**: https://github.com/HUBioDataLab/ProtHGT |
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--- |
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## What’s Inside |
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### data/ |
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PyTorch Geometric-compatible KG files: |
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- Full KG file (e.g., `prothgt-kg.pt`) |
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- Train/validation/test splits (e.g., `prothgt-*-graph.pt`) |
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- Alternative KG versions under `alternative_protein_embeddings/` (e.g., `esm2/`, `prott5/`), where the protein node features differ by embedding type. |
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**Available Files** |
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``` |
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├── prothgt-kg.pt # The default full knowledge graph containing TAPE embeddings as the initial protein representations. |
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├── prothgt-train-graph.pt # Training set (80% of the default full KG). |
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├── prothgt-val-graph.pt # Validation set (10% of the default full KG). |
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├── prothgt-test-graph.pt # Test set (10% of the default full KG). |
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└── alternative_protein_embeddings/ # Contains alternative KGs with different protein representations. |
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├──apaac/ |
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│ └── ... |
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├──esm2/ |
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│ └── ... |
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└──prott5/ |
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└── ... |
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``` |
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### models/ |
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Pretrained ProtHGT models (`.pt`). Models are provided: |
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- per GO sub-ontology (e.g., Molecular Function / Biological Process / Cellular Component) |
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- per protein embedding type (default vs `esm2` / `prott5` / etc.) |
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**Important:** Use a model checkpoint that matches the KG embedding variant you are using. |
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**Available Files** |
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``` |
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├── prothgt-model-molecular-function.pt # Pretrained ProtHGT checkpoint for Molecular Function (default/TAPE-based KG). |
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├── prothgt-model-biological-process.pt # Pretrained ProtHGT checkpoint for Biological Process (default/TAPE-based KG). |
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├── prothgt-model-cellular-component.pt # Pretrained ProtHGT checkpoint for Cellular Component (default/TAPE-based KG). |
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└── alternative_protein_embeddings/ # Models trained with alternative protein representations. |
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├── esm2/ |
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│ └── ... |
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└── prott5/ |
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└── ... |
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``` |
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--- |
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### How to Use (Training & Prediction) |
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To train or run inference, follow the instructions in the GitHub repository: https://github.com/HUBioDataLab/ProtHGT |
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Key scripts: |
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- `train.py` — trains ProtHGT using the provided KG splits |
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- `predict.py` — runs inference using pretrained checkpoints |
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--- |
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### Citation |
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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: |
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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) |
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--- |
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### Licensing |
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Copyright (C) 2025 HUBioDataLab |
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This dataset is released under GPL-3.0. |
