PhyloM

You can get the code for different parts of this project using the following command.

git clone https://github.com/algo-cancer/PhyloM.git

The list of packages and their version installed in our system for running these codes is provided in the packages.txt file. For data construction, the ms program is required from https://uchicago.app.box.com/s/l3e5uf13tikfjm7e1il1eujitlsjdx13. This program should be compiled based on its own instruction.

Branching Inference

The code for this part is placed under Branching_Inference folder.

See https://github.com/algo-cancer/PhyloM/blob/master/Branching_Inference/README.md for the instructions.

Noise Inference

The code for this part has been provided under Noise_Inference folder. See https://github.com/algo-cancer/PhyloM/blob/master/Noise_Inference/README.md for the instructions.

Noise Elimination

The code for this part could be found under Noise_Elimination folder. See https://github.com/algo-cancer/PhyloM/blob/master/Noise_Elimination/README.md for the instructions.

System configs

All the experiments in this work are performed using Carbonate, a computer cluster at Indiana University. We used deep learning (DL) nodes in Carbonate. These nodes features 12 GPU-accelerated Lenovo ThinkSystem SD530 , each equipped with two Intel Xeon Gold 6126 12-core CPUs, two NVIDIA GPU accelerators (eight with Tesla P100s; four with Tesla V100s), and 192 GB of RAM. A Red Hat Enterprise 7.x is running on these nodes and we used Python 3.7.3 :: Anaconda, Inc., Tensorflow 1.13.1, and Keras 2.2.4.

Contact

Please email us at esadeqia@iu.edu or mhaghir@iu.edu for any questions.