HVUE v2: leakage-controlled benchmark release

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README.md

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+---
+license: mit
+task_categories:
+  - text-classification
+language:
+  - en
+tags:
+  - biology
+  - genomics
+  - virology
+  - dna
+  - virus
+  - foundation-model
+  - benchmark
+pretty_name: "HVUE v2: Human Virome Understanding Evaluation Benchmark"
+---
+
+# HVUE v2: Human Virome Understanding Evaluation Benchmark
+
+> ⚠️ **This is version 2 of the HVUE benchmark.** Version 1 ([duttaprat/HVUE](https://huggingface.co/datasets/duttaprat/HVUE)) contained train-test sequence overlap due to chunk-level random splitting before clustering. HVUE v2 corrects this with cluster-aware splitting and verified zero leakage. **All v1 results should be considered superseded.**
+
+## Overview
+
+HVUE v2 is a rigorously constructed benchmark for evaluating DNA language models on three epidemiologically relevant viral prediction tasks:
+
+1. **Pathogenicity Classification** — Distinguishing disease-causing from benign viral strains
+2. **Transmissibility Prediction** — R₀-based classification (R₀ < 1 vs. R₀ ≥ 1)
+3. **Host Tropism Prediction** — Identifying human-infecting viruses from non-human-tropic viruses
+
+## Six-Stage Pipeline
+
+HVUE v2 eliminates train-test overlap through a six-stage pipeline:
+
+1. **Consolidation:** Source genomes collected and deduplicated at genome level
+2. **MMseqs2 Clustering:** Genomes clustered at 95% identity (standard) or 70% identity (hard)
+3. **Cluster-Aware Splitting:** Train/val/test splits (70/15/15) at the **cluster** level — all sequences in a cluster go to the same split
+4. **Chunking:** After splitting, genomes segmented into fixed-length windows (500/1000/2000 bp)
+5. **Deduplication:** SHA-256 hash-based exact-match removal within splits
+6. **Leakage Audit:** Automated verification of zero cross-split overlap
+
+**Key fix vs. v1:** Version 1 chunked first, then split randomly. Version 2 splits at the cluster level first, then chunks.
+
+## Configurations
+
+### Pathogenicity
+
+| Configuration | Description |
+|---|---|
+| `standard_capped_500bp` | Standard leakage-controlled benchmark, 500-bp fragments |
+| `standard_capped_1000bp` | Standard leakage-controlled benchmark, 1000-bp fragments |
+| `standard_capped_2000bp` | Standard leakage-controlled benchmark, 2000-bp fragments |
+| `hard_capped_1000bp` | More stringent hard-split benchmark, 1000-bp fragments |
+| `standard_temporal_1000bp` | Temporal benchmark, 1000-bp fragments |
+
+### Transmissibility
+
+| Configuration | Description |
+|---|---|
+| `standard_capped_500bp` | Standard leakage-controlled benchmark, 500-bp fragments |
+| `standard_capped_1000bp` | Standard leakage-controlled benchmark, 1000-bp fragments |
+| `standard_capped_2000bp` | Standard leakage-controlled benchmark, 2000-bp fragments |
+| `hard_capped_1000bp` | More stringent hard-split benchmark, 1000-bp fragments |
+| `standard_temporal_1000bp` | Temporal benchmark, 1000-bp fragments |
+
+### Host Tropism
+
+| Configuration | Description |
+|---|---|
+| `standard_95_500bp` | 95% cluster-aware benchmark, 500-bp fragments |
+| `standard_95_1000bp` | 95% cluster-aware benchmark, 1000-bp fragments |
+| `standard_95_2000bp` | 95% cluster-aware benchmark, 2000-bp fragments |
+| `hard_70_1000bp` | 70% cluster-aware hard benchmark, 1000-bp fragments |
+
+*Temporal splitting unavailable for Host Tropism (source data lacks collection-date metadata).*
+
+## Directory Structure
+
+```
+HVUE-v2/
+├── Pathogenicity/
+│   ├── standard_capped_500bp/
+│   ├── standard_capped_1000bp/
+│   │   ├── train.csv
+│   │   ├── dev.csv
+│   │   └── test.csv
+│   ├── standard_capped_2000bp/
+│   ├── hard_capped_1000bp/
+│   └── standard_temporal_1000bp/
+├── Transmissibility/
+│   └── ...
+├── Host_Tropism/
+│   ├── standard_95_500bp/
+│   ├── standard_95_1000bp/
+│   ├── standard_95_2000bp/
+│   └── hard_70_1000bp/
+└── README.md
+```
+
+## CSV Format
+
+Each CSV contains two columns:
+- `sequence`: DNA sequence (A/T/G/C)
+- `label`: Binary label (0 or 1)
+
+## Usage
+
+```python
+import pandas as pd
+from datasets import load_dataset
+
+# Load a specific config
+ds = load_dataset("duttaprat/HVUE-v2",
+                  data_dir="Pathogenicity/standard_capped_1000bp",
+                  data_files={"train": "train.csv", "validation": "dev.csv", "test": "test.csv"})
+
+# Or load directly
+train = pd.read_csv("Pathogenicity/standard_capped_1000bp/train.csv")
+```
+
+## Leakage Audit
+
+Zero exact-match or near-match overlap confirmed across all configurations. Audit scripts available at: https://github.com/duttaprat/HViLM
+
+## Citation
+
+```bibtex
+@article{dutta2026hvilm,
+  title={HViLM: A Foundation Model for Viral Genomics Enables Multi-Task Prediction of Pathogenicity, Transmissibility, and Host Tropism},
+  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.},
+  journal={mSystems},
+  year={2026}
+}
+```
+
+## License
+
+MIT License
+
+## Related Resources
+
+- **HViLM model weights:** [duttaprat/HViLM-base](https://huggingface.co/duttaprat/HViLM-base)
+- **Code:** [github.com/duttaprat/HViLM](https://github.com/duttaprat/HViLM)
+- **HVUE v1 (deprecated):** [duttaprat/HVUE](https://huggingface.co/datasets/duttaprat/HVUE)

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