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README.md

COS424 Final Project

Our final project is an extension to the second assignment, in which we aim to impute the methylation values along an entire chromosome genome sequence for a sparsely-sampled tissue based of 34 samples from other tissues. The 34 given samples are densely-sampled.

4 of the 34 samples were pathological, and thus not used in the model.

Overall methodology.

We try to fit a GMM model with off-diagonal bands as nonzero covariances. This is hard because default GMM implementations do not suffice for fitting this model on such a large dataset (each tissue sample has on the order of ~380K values).

We moved away from the off-diagonal model, relying only on the diagonal bands instead. See the paper for justification of the decision.

Directory description

A first-level data/ directory may be formed locally with cached computation data or unzipped raw data. This is intentionally git-ignored so that the repository does not store cacheable values.

The methylation-imputation/ directory is the Assigment 2 directory with starter code and zipped raw data. It is a submodule.

The utils/ directory contains various factored helper functions.

The paper.pdf file contains the submitted final paper.

The first-level of the git directory contains various jupyter notebooks that run the models in our paper in addition to the directories named above.

Installation

Dependencies

All the code uses Python 3; we assume typical machine learning libraries such as pandas, numpy, scikit-learn, etc. Please install them on-demand.

Notice on git clone

Use git clone --recursive ... instead of just git clone so that the submodule containig the original compressed data is retained.

Tasks

cycles Environment Setup

  1. Make sure you have a folder named just by your netid
  2. clone the repo inside of that folder (https://github.com/PrincetonUniversity/final-proj-cos-424)

cycles Environment Usage

  1. When you cd inside to the cyc424 in cycles, run source py/bin/activate to get a python3 env with sklearn.
  2. Make sure to use tmux to keep your computations alive
  3. Make changes only in the cloned repo in your personal folder so you don't interfere with others' stuff, then push it when it's ready. Don't push broken code.
  4. To use a jupyter notebook server hosted on cycles (but have graphical browser access on your local machine), see below section.

Remote jupyter notebook setup

Let PORT be some unused socket number (choose something between 10000 and 15000).

  1. ssh into cycles with the ssh option -L8888:localhost:$PORT
  2. Set up your cycles environment (including activating the virtual Python environment).
  3. In the directory containing the notebook you wish to edit, run jupyter notebook --no-browser --port=$PORT
  4. Open your browser locally, and navigate to localhost:8888
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