Datasets:
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README.md
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license: cc-by-nc-4.0
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---
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license: cc-by-nc-4.0
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task_categories:
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- tabular-classification
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tags:
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- biology
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- medical
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- genomics
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- genetics
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- bioinformatics
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pretty_name: Genetic Variant Pathogenicity Classification
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size_categories:
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- 10K<n<100K
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---
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# Genetic Variant Pathogenicity Dataset
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## Dataset Description
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This dataset contains annotated genetic variants (mutations) designed for tabular binary classification tasks. The objective is to predict whether a given genetic variant is **Pathogenic** (disease-causing) or **Benign** (harmless) based on a rich set of bioinformatics annotations, evolutionary conservation scores, and functional prediction tools.
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- **Task:** Binary Classification
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- **Target Column:** `Pathologic/Benign`
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## Dataset Structure
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The dataset is pre-split into `train` and `test` sets, making it ready for immediate machine learning modeling. The class distribution is highly balanced.
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| Split | Number of Rows | Benign Count | Pathogenic Count |
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|-------|----------------|--------------|------------------|
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| Train | 7,856 | 3,940 | 3,916 |
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| Test | 4,910 | 2,460 | 2,450 |
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## Key Features
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The dataset consists of 69 columns. While it includes extensive biological data, some of the most critical feature categories include:
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* **Variant Identifiers:** `Chrom`, `Position`, `Ref Base`, `Alt Base`, `Gene`
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* **Molecular Consequences:** `Sequence Ontology` (e.g., *missense_variant*), `cDNA change`, `Protein Change`
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* **Population Frequencies:** Allele frequencies from the 1000 Genomes Project and ESP6500.
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* **Functional Prediction Scores:** `CADD Exome Score`, `PolyPhen-2`, `SIFT`, `REVEL Score`
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* **Conservation Scores:** `GERP++`, `PhyloP`, `SiPhy`
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* **Target Label:** `Pathologic/Benign` (Values: "Benign" or "Pathogenic")
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## Usage
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You can easily load and explore this dataset using the Hugging Face `datasets` library:
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```python
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from datasets import load_dataset
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# Load the dataset (replace 'your-username' with your actual Hugging Face username)
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dataset = load_dataset("your-username/genetic-variant-pathogenicity")
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# View the dataset structure
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print(dataset)
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# Convert the train split to a Pandas DataFrame for easy manipulation
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df_train = dataset['train'].to_pandas()
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print(df_train['Pathologic/Benign'].value_counts())
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