Instructions to use duttaprat/HViLM-Patho with libraries, inference providers, notebooks, and local apps. Follow these links to get started.
- Libraries
- Transformers
How to use duttaprat/HViLM-Patho with Transformers:
# Use a pipeline as a high-level helper from transformers import pipeline pipe = pipeline("text-classification", model="duttaprat/HViLM-Patho", trust_remote_code=True)# pip install -U transformers accelerate # Load model directly from transformers import AutoModelForSequenceClassification model = AutoModelForSequenceClassification.from_pretrained("duttaprat/HViLM-Patho", trust_remote_code=True, device_map="auto") - Notebooks
- Google Colab
- Kaggle
Update README.md
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README.md
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library_name: transformers
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base_model: duttaprat/HViLM-base
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datasets:
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- duttaprat/HVUE
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pipeline_tag: text-classification
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tags:
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- genomics
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- dna
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- virus
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- pathogenicity
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- hvue
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license: apache-2.0
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---
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**HViLM-Patho** is the official HViLM model for binary virus pathogenicity classification.
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- **Fine-tuned from:** [duttaprat/HViLM-base](https://huggingface.co/duttaprat/HViLM-base)
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- **Benchmark:** [duttaprat/HVUE
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- **HVUE
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- **Checkpoint selection:** best validation F1 (`checkpoint-3000`)
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- **Input:** virus nucleotide sequence
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- **Output:** non-pathogenic vs. pathogenic
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## Performance
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Held-out HVUE
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| Metric | Score |
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- [HViLM-base](https://huggingface.co/duttaprat/HViLM-base)
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- [HViLM-R0](https://huggingface.co/duttaprat/HViLM-R0)
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- [HViLM-Tropism](https://huggingface.co/duttaprat/HViLM-Tropism)
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- [HVUE
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- [HViLM GitHub repository](https://github.com/duttaprat/HViLM)
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## Citation
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library_name: transformers
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base_model: duttaprat/HViLM-base
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datasets:
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- duttaprat/HVUE
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pipeline_tag: text-classification
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tags:
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- genomics
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- dna
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- virus
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- pathogenicity
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- hvue
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license: apache-2.0
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---
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**HViLM-Patho** is the official HViLM model for binary virus pathogenicity classification.
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- **Fine-tuned from:** [duttaprat/HViLM-base](https://huggingface.co/duttaprat/HViLM-base)
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- **Benchmark:** [duttaprat/HVUE](https://huggingface.co/datasets/duttaprat/HVUE)
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- **HVUE configuration:** `Pathogenicity/standard_capped_1000bp`
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- **Checkpoint selection:** best validation F1 (`checkpoint-3000`)
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- **Input:** virus nucleotide sequence
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- **Output:** non-pathogenic vs. pathogenic
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## Performance
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Held-out HVUE test set, standard 1000-nt configuration:
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| Metric | Score |
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|---|---:|
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- [HViLM-base](https://huggingface.co/duttaprat/HViLM-base)
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- [HViLM-R0](https://huggingface.co/duttaprat/HViLM-R0)
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- [HViLM-Tropism](https://huggingface.co/duttaprat/HViLM-Tropism)
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- [HVUE](https://huggingface.co/datasets/duttaprat/HVUE)
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- [HViLM GitHub repository](https://github.com/duttaprat/HViLM)
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## Citation
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