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  HVUE (Human Virome Understanding Evaluation) is a comprehensive benchmark for evaluating foundation models on viral genomics tasks. The benchmark comprises 7 curated datasets across 3 epidemiologically critical prediction tasks:
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- - **Pathogenicity Classification** (3 datasets, ~50,000 sequences)
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- - **Host Tropism Prediction** (1 dataset, 9,428 sequences)
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- - **Transmissibility Assessment** (3 datasets, ~7,300 sequences)
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  **Paper**: *HViLM: A Foundation Model for Viral Genomics Enables Multi-Task Prediction of Pathogenicity, Transmissibility, and Host Tropism*
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  ## Data Format
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  Each dataset contains three splits:
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- - `train.csv` (70%)
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- - `dev.csv` (15%)
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- - `test.csv` (15%)
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  CSV columns:
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  - `sequence`: Viral genomic sequence (250-1000 bp)
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  train_data = load_dataset("duttaprat/HVUE", data_files="pathogenicity/CINI/train.csv")
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  ```
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- ## Data Leakage Prevention
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- Systematic overlap analysis was performed between pre-training data (VIRION database) and HVUE benchmark:
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- - Method: Accession ID matching + MMseqs2 similarity (>95% identity)
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- - Result: 186 overlapping sequences removed from pre-training corpus
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- - Clean separation between pre-training and evaluation data
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  ## Citation
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  ```bibtex
 
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  HVUE (Human Virome Understanding Evaluation) is a comprehensive benchmark for evaluating foundation models on viral genomics tasks. The benchmark comprises 7 curated datasets across 3 epidemiologically critical prediction tasks:
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+ - **Pathogenicity Classification** (3 datasets)
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+ - **Host Tropism Prediction** (1 dataset)
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+ - **Transmissibility Assessment** (3 datasets)
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  **Paper**: *HViLM: A Foundation Model for Viral Genomics Enables Multi-Task Prediction of Pathogenicity, Transmissibility, and Host Tropism*
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  ## Data Format
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  Each dataset contains three splits:
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+ - `train.csv`
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+ - `dev.csv`
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+ - `test.csv`
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  CSV columns:
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  - `sequence`: Viral genomic sequence (250-1000 bp)
 
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  train_data = load_dataset("duttaprat/HVUE", data_files="pathogenicity/CINI/train.csv")
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  ```
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  ## Citation
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  ```bibtex