microsoft
/
normalized_trend_filtering
зеркало из
1
0
Форкнуть 0
Код Задачи Пакеты Проекты Релизы Вики Активность
Normalized Trend Filtering for Biomedical Datasets
7 коммитов 3 Ветки 0 Теги 19 MiB
Jupyter Notebook 98.3%
Python 1.7%
Перейти к файлу
hugh eb73f12424
Update SECURITY.md 
init changes
 		2020-12-04 13:46:45 -05:00
data init commits to ntf 2020-12-04 13:40:22 -05:00
notebooks init commits to ntf 2020-12-04 13:40:22 -05:00
utils init commits to ntf 2020-12-04 13:40:22 -05:00
.gitignore init commits to ntf 2020-12-04 13:40:22 -05:00
CODE_OF_CONDUCT.md Initial CODE_OF_CONDUCT.md commit 2020-12-04 10:27:54 -08:00
LICENSE Initial LICENSE commit 2020-12-04 10:27:56 -08:00
README.md init commits to ntf 2020-12-04 13:40:22 -05:00
README_temp.md init commits to ntf 2020-12-04 13:40:22 -05:00
SECURITY.md Update SECURITY.md 2020-12-04 13:46:45 -05:00
SUPPORT.md Initial SUPPORT.md commit 2020-12-04 10:27:58 -08:00
requirements.txt init commits to ntf 2020-12-04 13:40:22 -05:00

README.md

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