Update README.md

README.md

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----
-license: gpl-3.0
----
+---
+license: gpl-3.0
+tags:
+- biology
+pretty_name: 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.