Personalized Medicine: Redefining Cancer Treatment

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Usage

1. Clone the repo

git clone [email protected]:dujm/Health_PrecisionMedicine.git

# Remove my git directory
cd Health_PrecisionMedicine
rm -r .git/

# Create a src/ dir to save models
mkdir src

# Create a data/ to download and save datasets
mkdir data

2. Install packages

pip install -r requirements.txt

3. Download the Kaggle dataset

• Download from Kaggle Website

• Or install Kaggle API and run:

  cd data
  
  # Download data
  kaggle competitions download msk-redefining-cancer-treatment
  

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Files

 ├── LICENSE
 ├── README.md
 ├── requirements.txt   
 ├── data (Not uploaded to GitHub)
 │   ├── features
 │   ├── history
 │   ├── processed
 │   └── raw
 │       ├── test_text
 │       ├── test_variants
 │       ├── training_text
 │       ├──training_variants
 │       └── not_used
 ├── notebooks
 │   ├── 01EDA.ipynb
 │   ├── 02Test_Sample_Data.ipynb
 │   ├── 03BoW_Full_Data.ipynb
 │   ├── 04Word2Vec_LSTM_Full_Data.ipynb
 │   ├── 05Doc2Vec_Keras_Full_Data.ipynb  
 │   └── utils_functions.py
 ├── reports
 │   ├── figures
 │   └── materials
 ├── src (Not uploaded to GitHub)
 │   ├── doc2vec
 └── └── word2vec

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References

• Personalized Medicine: Redefining Cancer Treatment
• A simple anaysis of the dataset using nltk and Word2Vec
• Basic NLP
• Paweł Jankiewicz