Here are the software scripts implementing our machine learning methods for multi-ancestral clinico-genomic prediction of diseases.
Entity Path/location Note
Data ./data/instructions.txt The path of the real and synthetic datasets.
Model ./*.py/build_model The interface used to build generator a deep learning model with Keras.
Mixture ./scripts/*.py/mixture_learning The mixture learning scheme for each study.
Independent ./scripts/*.py/independent_learning The independent learning scheme for each study
Naïve ./scripts/*.py/naive_transfer The Naïve transfer learning Transfer scheme for each study
Transfer ./scripts/*.py/super_transfer The transfer learning scheme for each study
TL_PRS ./script/LR/TL_PRS.py The implementation of the linear transfer method.
The system relies on the following software, reagent, or resources.
Our software has been tested on the following software version.
Software and SOURCE IDENTIFIER Hardware
REAGENT or RESOURCE SOURCE IDENTIFIER
Python 3.7 Python Software https://www.python.org/download/releases/2.7/ Foundation
Numpy 1.15.4 Tidelift, Inc https://libraries.io/pypi/numpy/1.15.4
Numpydoc 0.9.1 Tidelift, Inc https://libraries.io/pypi/numpydoc
Scipy 1.2.1 The SciPy https://docs.scipy.org/doc/scipy-1.2.1/reference/ community
Sklearn 0.0 The Python https://pypi.org/project/sklearn/ community
Keras 2.2.4 GitHub, Inc. https://github.com/keras-team/keras/releases/tag/2.2.4
Keras-Applications GitHub, Inc. https://github.com/keras-team/keras-applications 1.0.8
Keras-Preprocessing GitHub, Inc. https://github.com/keras-team/keras-preprocessing/releases/tag/1.1.0 1.1.0
Tensorboard 1.13.1 GitHub, Inc. https://github.com/tensorflow/tensorboard/releases/tag/1.13.1
Tensorflow 1.13.1 tensorflow.org https://www.tensorflow.org/install/pip
Tensorflow-estimator The Python https://pypi.org/project/tensorflow-estimator/ 1.13.1 community
Statsmodels 0.9.0 Statsmodels.org https://www.statsmodels.org/stable/release/version0.9.html
Xlrd 1.2.0 The Python https://pypi.org/project/xlrd/ community
XlsxWriter 1.1.8 The Python https://pypi.org/project/XlsxWriter/ community
Xlwings 0.15.8 The Python https://pypi.org/project/xlwings/
community
Xlwt 1.3.0 The Python https://pypi.org/project/xlwt/
community
We recommend using a GPU (V100) for optimal software performance.
This package contains the source code and instructions to reproduce the results represented in our paper. Our software would run on Windows and Ubuntu, but we suggest using Linux system which is easier for environment configuration.
Conda --install requirements.txt
Requirements.txt
numpy==1.15.4
numpydoc==0.9.1
scipy==1.2.1
seaborn==0.9.0
sklearn==0.0
skrebate==0.6
torch==1.7.1
Keras==2.2.4
Keras-Applications==1.0.8
Keras-Preprocessing==1.1.0
tensorboard==1.13.1
tensorflow==1.13.1
tensorflow-estimator==1.13.0
statsmodels==0.9.0
lifelines==0.16.3
Optunity==1.1.1
xlrd==1.2.0-
XlsxWriter==1.1.8
xlwings==0.15.8
xlwt==1.3.0
Yan Gao and Yan Cui, ({ygao45, ycui2}@uthsc.edu).
This project is covered under the GNU General Public License (GPL).