Viro-BERT

Whole-genome Transformer framework for viral pathogen classification across 14 viral classes using Chunk-and-Vote Late Fusion Consensus.

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Requirements

pip install torch transformers biopython

Tested on Python 3.8+ and PyTorch 1.13+ (supports CPU and CUDA).

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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.

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Command-Line Usage (Python)

Classify viral sequences from a FASTA file:

python predict.py --fasta sample.fasta

Optional arguments:

python predict.py --fasta sample.fasta --weights sota_chunk_model.pth --config config.json --top_k 3 --cpu

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Execution via R

Run directly from an R environment via system command:

system("python predict.py --fasta sample.fasta")

Or programmatically via the reticulate interface:

library(reticulate)
py_run_file("predict.py")

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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)

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License

Open access under the MIT License.