| --- |
| license: mit |
| language: |
| - en |
| tags: |
| - biology |
| - genomics |
| - viral-classification |
| - transformer |
| - distilbert |
| --- |
| |
| # Viro-BERT |
|
|
| Whole-genome Transformer framework for viral pathogen classification across 14 viral classes using Chunk-and-Vote Late Fusion Consensus. |
|
|
| --- |
|
|
| ### Requirements |
|
|
| ```bash |
| pip install torch transformers biopython |
| |
| ``` |
|
|
| Tested on Python 3.8+ and PyTorch 1.13+ (supports CPU and CUDA). |
|
|
| --- |
|
|
| ### Files in Repository |
|
|
| * `sota_chunk_model.pth` — Trained PyTorch model weights (DistilBERT backbone, 6 layers, 12 heads, hidden dim 768). |
| * `config.json` — 130-token 3-mer vocabulary, hyperparameters, and 14 target class mappings. |
| * `predict.py` — Standalone inference script for FASTA sequence classification. |
|
|
| --- |
|
|
| ### Command-Line Usage (Python) |
|
|
| Classify viral sequences from a FASTA file: |
|
|
| ```bash |
| python predict.py --fasta sample.fasta |
| |
| ``` |
|
|
| Optional arguments: |
|
|
| ```bash |
| python predict.py --fasta sample.fasta --weights sota_chunk_model.pth --config config.json --top_k 3 --cpu |
| |
| ``` |
|
|
| --- |
|
|
| ### Execution via R |
|
|
| Run directly from an R environment via system command: |
|
|
| ```R |
| system("python predict.py --fasta sample.fasta") |
| |
| ``` |
|
|
| Or programmatically via the `reticulate` interface: |
|
|
| ```R |
| library(reticulate) |
| py_run_file("predict.py") |
| |
| ``` |
|
|
| --- |
|
|
| ### Target Viral Classes (14) |
|
|
| * Dengue Virus (`Dengue`) |
| * Enterovirus A (`EnteroA`) |
| * Enterovirus B (`EnteroB`) |
| * Hepatitis B Virus (`HBV`) |
| * Hepatitis C Virus (`HCV`) |
| * Human Papillomavirus (`HPV`) |
| * Human Alphaherpesvirus 1 (`HSV-1`) |
| * Influenza A Virus (`IAV`) |
| * Influenza B Virus (`IBV`) |
| * Influenza C Virus (`ICV`) |
| * Monkeypox Virus (`MPV`) |
| * Severe Fever with Thrombocytopenia Syndrome Virus (`SFTS`) |
| * West Nile Virus (`WNV`) |
| * Zika Virus (`Zika`) |
|
|
| --- |
|
|
| ### License |
|
|
| Open access under the MIT License. |
|
|
| ``` |
| |
| ``` |
