Normalized Trend Filtering for Biomedical Datasets

Requirements

Install required modules with:

bash
conda create -n NTF python=3.7 numpy=1.18.1 mkl_random=1.1.0
conda activate NTF
pip install -r requirements.txt

Introduction

Associated paper can be found here:

Data

Paper and datasets used for empirical study:

• Harel_PD1: DATA, PAPER

• Harel_TIL: DATA, PAPER

• VanAllen: RNA-seq DATA, RESPONSE, PAPER

• OpenPBTA: DATA, PAPER
  Follow data download instructions from OpenPBTA (ver. release-v9-20191105)
  RNA-seq data is found in "pbta-gene-expression-kallisto.stranded.rds"
  Response is found in "pbta-histologies.tsv"

• inBiomap Interactome: DATA, PAPER

Notebooks

Notebooks produce the network figures and Tables 1. and 2.

DATASET.ipynb contains analysis for Lasso, MCP, SCAD, Ridge, GraphTF, NTF-Lasso, NTF-MCP, NTF-SCAD, Laplacian Ridge, and Shuffled Experiments

DATASET_LapRidge.ipynb contains analysis for Lasso + Laplacian Ridge, MCP + Laplacian Ridge, SCAD + Laplacian Ridge