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README.md

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+---
+license: cc-by-nc-nd-4.0
+task_categories:
+- other
+tags:
+- chemistry
+- mass-spectrometry
+- DOM
+- formula-assignment
+- knn
+pretty_name: DOM Formula Assignment Dataset
+size_categories:
+- n<1K
+---
+
+# DOM Formula Assignment Dataset
+
+This dataset contains training and testing data for Dissolved Organic Matter (DOM) formula assignment using K-Nearest Neighbors (KNN) machine learning models.
+
+## Dataset Description
+
+The dataset includes mass spectrometry data from different sources and instruments used to train and evaluate KNN models for automated molecular formula assignment in DOM samples.
+
+### Dataset Structure
+
+```
+├── DOM_training_set_ver2/          # 7T FT-ICR MS training data
+│   ├── Table_Harney_River_*.xlsx   # Harney River samples (5 files)
+│   ├── Table_Pantanal_*.xlsx       # Pantanal samples (2 files)
+│   ├── Table_Suwannee_River_Fulvic_Acid_2.xlsx
+│   └── Families_Tables/            # Chemical family classifications
+│       ├── Families-Short-hr1.csv
+│       ├── Families-Short-hr5.csv
+│       ├── Families-Short-pantanal.csv
+│       └── Families-Short-srfa.csv
+│
+├── DOM_training_set_ver3/          # 21T FT-ICR MS training data
+│   ├── Table_Harney_River_*_21T.xlsx   # 21T Harney River samples (5 files)
+│   └── Table_Suwannee_River_Fulvic_Acid_2_21T.xlsx
+│
+├── synthetic_data/                 # Synthetic formula combinations
+│   └── formula_combinations_*.csv  # 51 files covering m/z ranges 100-610
+│
+├── DOM_testing_set/               # Testing samples
+│   ├── Table_Pahokee_River_Fulvic_Acid.xlsx
+│   ├── Table_Suwannee_River_Fulvic_Acid_2_v2.xlsx
+│   └── Table_Suwannee_River_Fulvic_Acid_3.xlsx
+│
+├── DOM_testing_set_Peaklists/     # Detailed peaklists for testing
+│   ├── PPFA/                       # Pahokee Peat Fulvic Acid
+│   ├── SRFA2/                      # Suwannee River Fulvic Acid 2
+│   └── SRFA3/                      # Suwannee River Fulvic Acid 3
+│
+└── knn_comparison_summary.csv     # Model performance comparison results
+```
+
+## Data Sources
+
+### Training Data
+
+- **7T FT-ICR MS Data (ver2)**: High-resolution mass spectrometry data from a 7 Tesla instrument
+  - 8 Excel files with assigned formulas
+  - Chemical family classification tables
+  
+- **21T FT-ICR MS Data (ver3)**: Ultra-high resolution data from a 21 Tesla instrument
+  - 6 Excel files with assigned formulas
+  - Higher mass accuracy and resolution
+
+- **Synthetic Data**: Computationally generated formula combinations
+  - 51 CSV files covering m/z range 100-610 Da
+  - Used to expand training coverage for underrepresented m/z regions
+
+### Testing Data
+
+- **DOM Testing Set**: Independent samples for model validation
+  - Pahokee Peat Fulvic Acid (PPFA)
+  - Suwannee River Fulvic Acid standards (SRFA2, SRFA3)
+  
+- **Peaklists**: Detailed peak information with multiple acquisition methods
+  - Different pulse sequences (aFTk, aFTsk, dmFTk)
+  - CSV format with m/z and intensity data
+
+## Data Format
+
+### Excel Files (.xlsx)
+Training and testing files contain:
+- m/z values (mass-to-charge ratios)
+- Assigned molecular formulas (C, H, O, N, S counts)
+- Additional metadata depending on the sample
+
+### CSV Files
+- **Peaklists**: m/z, intensity, and spectral information
+- **Synthetic data**: Formula combinations with element counts
+- **Families tables**: Chemical family classifications
+- **Comparison summary**: Model performance metrics
+
+## Usage
+
+This dataset is designed to be used with the DOM KNN models available at:
+[bilalsm/dom-formula-assignment-using-knn](https://huggingface.co/bilalsm/dom-formula-assignment-using-knn)
+
+### Loading the Dataset
+
+```python
+from huggingface_hub import hf_hub_download
+import pandas as pd
+
+# Download a specific file
+file_path = hf_hub_download(
+    repo_id="bilalsm/dom-formula-assignment-data",
+    filename="knn_comparison_summary.csv",
+    repo_type="dataset"
+)
+
+# Load with pandas
+df = pd.read_csv(file_path)
+print(df.head())
+```
+
+### Download Entire Dataset
+
+```python
+from huggingface_hub import snapshot_download
+
+# Download all data
+data_path = snapshot_download(
+    repo_id="bilalsm/dom-formula-assignment-data",
+    repo_type="dataset"
+)
+print(f"Dataset downloaded to: {data_path}")
+```
+
+## Statistics
+
+- **Total files**: ~82 files (17 Excel, 65 CSV)
+- **Total size**: ~73 MB
+- **Training samples**: 
+  - 8 files (7T data)
+  - 6 files (21T data)
+  - 51 synthetic files
+- **Testing samples**: 3 independent DOM samples
+- **Peaklists**: 9 detailed acquisition files
+
+## Model Performance
+
+The models trained on this dataset achieve:
+
+| Model Type | Assignment Rate | Accuracy |
+|-----------|----------------|----------|
+| Synthetic (synthetic_data) | 99.975% | 99.65% |
+| 7T-21T Ensemble (ver2 + ver3) | 95.355% | 99.84% |
+| 7T Only (ver2) | 81.815% | 99.84% |
+| 21T Only (ver3) | 81.815% | 99.84% |
+
+See `knn_comparison_summary.csv` for detailed results across all model variants.
+
+## Citation
+
+This dataset supports research on automated formula assignment in DOM analysis using machine learning. A manuscript describing the methodology is currently under review.
+
+## License
+
+This dataset is released under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC BY-NC-ND 4.0).
+
+## Contact
+
+For questions or issues with the dataset, please open an issue on the model repository or contact the authors.
+
+## Related Resources
+
+- **Model Repository**: [bilalsm/dom-formula-assignment-using-knn](https://huggingface.co/bilalsm/dom-formula-assignment-using-knn)
+- **GitHub Repository**: [pcdslab/dom-formula-assignment-using-ml](https://github.com/pcdslab/dom-formula-assignment-using-ml)