Feature Extraction
Transformers
PyTorch
English
fill-mask
genomics
virology
dnabert
foundation-model
hvilm
viral-genomics
pathogenicity
transmissibility
host-tropism
hvue
custom_code
Instructions to use duttaprat/HViLM-base with libraries, inference providers, notebooks, and local apps. Follow these links to get started.
- Libraries
- Transformers
How to use duttaprat/HViLM-base with Transformers:
# Use a pipeline as a high-level helper from transformers import pipeline pipe = pipeline("feature-extraction", model="duttaprat/HViLM-base", trust_remote_code=True)# pip install -U transformers accelerate # Load model directly from transformers import AutoModelForMaskedLM model = AutoModelForMaskedLM.from_pretrained("duttaprat/HViLM-base", trust_remote_code=True, device_map="auto") - Notebooks
- Google Colab
- Kaggle
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## Citation
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If you use DNABERT-2 (the base model), please also cite:
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```bibtex
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@article{zhou2023dnabert2,
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title={DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome},
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author={Zhou, Zhihan and Ji, Yanrong and Li, Weijian and Dutta, Pratik and Davuluri, Ramana and Liu, Han},
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journal={ICLR},
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year={2024}
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}
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```
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If you use HViLM in your research, please cite our paper:
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@article{dutta2026hvilm,
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title={HViLM: A foundation model for viral genomics enables multi-task prediction of pathogenicity, transmissibility, and host tropism},
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author={Dutta, Pratik and Vaska, Jack and Surana, Pallavi and Sathian, Rekha and Chao, Max and Zhou, Zhihan and Liu, Han and Davuluri, Ramana V},
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## Citation
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If you use HViLM in your research, please cite our paper:
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```bibtex
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@article{dutta2026hvilm,
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title={HViLM: A foundation model for viral genomics enables multi-task prediction of pathogenicity, transmissibility, and host tropism},
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author={Dutta, Pratik and Vaska, Jack and Surana, Pallavi and Sathian, Rekha and Chao, Max and Zhou, Zhihan and Liu, Han and Davuluri, Ramana V},
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