Update README.md
Browse files
README.md
CHANGED
|
@@ -21,9 +21,9 @@ size_categories:
|
|
| 21 |
|
| 22 |
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:
|
| 23 |
|
| 24 |
-
- **Pathogenicity Classification** (3 datasets
|
| 25 |
-
- **Host Tropism Prediction** (1 dataset
|
| 26 |
-
- **Transmissibility Assessment** (3 datasets
|
| 27 |
|
| 28 |
**Paper**: *HViLM: A Foundation Model for Viral Genomics Enables Multi-Task Prediction of Pathogenicity, Transmissibility, and Host Tropism*
|
| 29 |
|
|
@@ -72,9 +72,9 @@ HVUE (Human Virome Understanding Evaluation) is a comprehensive benchmark for ev
|
|
| 72 |
## Data Format
|
| 73 |
|
| 74 |
Each dataset contains three splits:
|
| 75 |
-
- `train.csv`
|
| 76 |
-
- `dev.csv`
|
| 77 |
-
- `test.csv`
|
| 78 |
|
| 79 |
CSV columns:
|
| 80 |
- `sequence`: Viral genomic sequence (250-1000 bp)
|
|
@@ -94,12 +94,7 @@ patho_cini = load_dataset("duttaprat/HVUE", data_files="pathogenicity/CINI/*.csv
|
|
| 94 |
train_data = load_dataset("duttaprat/HVUE", data_files="pathogenicity/CINI/train.csv")
|
| 95 |
```
|
| 96 |
|
| 97 |
-
## Data Leakage Prevention
|
| 98 |
|
| 99 |
-
Systematic overlap analysis was performed between pre-training data (VIRION database) and HVUE benchmark:
|
| 100 |
-
- Method: Accession ID matching + MMseqs2 similarity (>95% identity)
|
| 101 |
-
- Result: 186 overlapping sequences removed from pre-training corpus
|
| 102 |
-
- Clean separation between pre-training and evaluation data
|
| 103 |
|
| 104 |
## Citation
|
| 105 |
```bibtex
|
|
|
|
| 21 |
|
| 22 |
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:
|
| 23 |
|
| 24 |
+
- **Pathogenicity Classification** (3 datasets)
|
| 25 |
+
- **Host Tropism Prediction** (1 dataset)
|
| 26 |
+
- **Transmissibility Assessment** (3 datasets)
|
| 27 |
|
| 28 |
**Paper**: *HViLM: A Foundation Model for Viral Genomics Enables Multi-Task Prediction of Pathogenicity, Transmissibility, and Host Tropism*
|
| 29 |
|
|
|
|
| 72 |
## Data Format
|
| 73 |
|
| 74 |
Each dataset contains three splits:
|
| 75 |
+
- `train.csv`
|
| 76 |
+
- `dev.csv`
|
| 77 |
+
- `test.csv`
|
| 78 |
|
| 79 |
CSV columns:
|
| 80 |
- `sequence`: Viral genomic sequence (250-1000 bp)
|
|
|
|
| 94 |
train_data = load_dataset("duttaprat/HVUE", data_files="pathogenicity/CINI/train.csv")
|
| 95 |
```
|
| 96 |
|
|
|
|
| 97 |
|
|
|
|
|
|
|
|
|
|
|
|
|
| 98 |
|
| 99 |
## Citation
|
| 100 |
```bibtex
|