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README.md

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+---
+license: mit
+task_categories:
+- text-classification
+tags:
+- tcr
+- tcr-pmhc
+- peptide
+- mhc
+- immunology
+- binding-prediction
+- pmt
+size_categories:
+- 100K<n<1M
+---
+
+# PMT Benchmark Dataset
+
+## Dataset Description
+
+The PMT (Peptide-MHC-TCR) benchmark dataset for training and evaluating TCR-pMHC binding prediction models. This dataset contains TCR CDR3 sequences, peptide antigens, HLA alleles, and binary binding labels.
+
+### Dataset Summary
+
+This is the official PMT training and in-distribution (ID) test set from the SPRINT framework. The data has been cleaned, deduplicated, and standardized for reproducibility.
+
+- **Training Set**: 474,881 samples
+- **ID Test Set**: 4,564 samples
+- **Task**: Binary classification (TCR-pMHC binding prediction)
+- **Modality**: TCR CDR3 + Peptide + MHC (PMT task)
+
+## Dataset Structure
+
+### Data Files
+
+- `train.csv`: Training data (474,881 samples)
+- `id_test.csv`: In-distribution test data (4,564 samples)
+
+### Data Format
+
+CSV files with the following columns:
+
+| Column | Type | Description |
+|--------|------|-------------|
+| CDR3 | string | TCR CDR3beta amino acid sequence |
+| peptide | string | Peptide antigen sequence (8-15 aa) |
+| HLA | string | HLA allele (standardized format: A*02:01) |
+| label | int | Binding label (1=binder, 0=non-binder) |
+| HLA_sequence | string | HLA pseudo-sequence (optional) |
+
+### Dataset Statistics
+
+#### Training Set
+
+- **Total Samples**: 474,881
+- **Positive Samples**: 33,129 (7.0%)
+- **Negative Samples**: 441,752 (93.0%)
+- **Unique HLAs**: 78
+- **Unique Peptides**: 638
+- **Unique TCRs**: 32,853
+
+#### ID Test Set
+
+- **Total Samples**: 4,564
+- **Positive Samples**: 321 (7.0%)
+- **Negative Samples**: 4,243 (93.0%)
+- **Unique HLAs**: 12
+- **Unique Peptides**: 190
+- **Unique TCRs**: 1,283
+
+## Usage
+
+### Load with Hugging Face Datasets
+
+```python
+from datasets import load_dataset
+
+# Load training data
+dataset = load_dataset("YYJMAY/pmt-interaction", split="train")
+train_df = dataset.to_pandas()
+
+# Load test data
+dataset = load_dataset("YYJMAY/pmt-interaction", split="test")
+test_df = dataset.to_pandas()
+```
+
+### Load with Pandas
+
+```python
+import pandas as pd
+from huggingface_hub import hf_hub_download
+
+# Download training file
+train_path = hf_hub_download(
+    repo_id="YYJMAY/pmt-interaction",
+    filename="train.csv",
+    repo_type="dataset"
+)
+train_df = pd.read_csv(train_path)
+
+# Download test file
+test_path = hf_hub_download(
+    repo_id="YYJMAY/pmt-interaction",
+    filename="id_test.csv",
+    repo_type="dataset"
+)
+test_df = pd.read_csv(test_path)
+```
+
+### Use with SPRINT Framework
+
+The SPRINT framework automatically downloads and uses this dataset:
+
+```bash
+python scripts/run_benchmark.py --method METHOD --dataset pmt --mode train
+python scripts/run_benchmark.py --method METHOD --dataset pmt --mode eval
+```
+
+## Data Quality
+
+### Preprocessing
+
+- **Deduplication**: All duplicate entries removed based on (CDR3, peptide, HLA, label)
+- **HLA Standardization**: All HLA alleles normalized to standard format (e.g., A*02:01)
+- **Missing Values**: No missing values in required columns
+- **Label Validation**: All labels are binary (0 or 1)
+
+### Peptide Length Distribution
+
+Training set peptide lengths: 8-15 amino acids
+Test set peptide lengths: 8-15 amino acids
+
+## Construction
+
+This dataset was curated and cleaned as part of the SPRINT benchmarking framework:
+
+1. Collected from multiple public TCR-pMHC datasets
+2. Standardized HLA allele naming conventions
+3. Removed duplicates and incomplete entries
+4. Split into training and in-distribution test sets
+5. Validated for data quality and consistency
+
+## Tasks
+
+This dataset is designed for:
+
+- **PMT (Peptide-MHC-TCR) Task**: Predict TCR-pMHC binding using all three components
+- **Binary Classification**: Classify as binder (1) or non-binder (0)
+- **Model Benchmarking**: Evaluate model performance on standardized data
+
+## Limitations
+
+- Only includes class I MHC (HLA-A, HLA-B, HLA-C)
+- Limited to TCR CDR3beta sequences
+- Binary labels (no binding affinity values)
+- Peptide length range: 8-15 amino acids
+
+## Citation
+
+If you use this dataset, please cite:
+
+```bibtex
+@dataset{pmt_benchmark_2024,
+  title={PMT Benchmark Dataset for TCR-pMHC Binding Prediction},
+  author={SPRINT Framework Contributors},
+  year={2024},
+  url={https://huggingface.co/datasets/YYJMAY/pmt-interaction}
+}
+```
+
+## License
+
+MIT License
+
+## Contact
+
+For questions or issues, please open an issue in the SPRINT repository.
+
+## Related Datasets
+
+- Allelic OOD: YYJMAY/allelic-ood
+- Temporal OOD: YYJMAY/temporal-ood
+- Modality OOD: YYJMAY/modality-ood