Quantification of tumor heterogeneity

Organized by magrichard - Current server time: Oct. 22, 2019, 6:01 a.m. UTC

First phase

Exploration
July 22, 2019, midnight UTC

End

Competition Ends
Aug. 23, 2019, 2 p.m. UTC

Successful treatment of cancer is still a challenge and this is partly due to a wide heterogeneity of cancer composition across patient population. Unfortunately, accounting for such heterogeneity is very difficult. Clinical evaluation of tumor heterogeneity often requires the expertise of anatomical pathologists and radiologists.

This challenge is dedicated to the quantification of intra-tumor heterogeneity using appropriate statistical methods on cancer omics data.

In particular, it focuses on estimating cell types and proportion in biological samples based on averaged DNA methylation and full patient history. The goal is to explore various statistical methods for source separation/deconvolution analysis (Non-negative Matrix Factorization, Surrogate Variable Analysis, Principal component Analysis, Latent Factor Models, …).

How to start?

[1] Go on the challenge page, in the Learn the details tab, in the get_starting_kit item and download the starting kit by clicking the Starting Kit button.

[2] On your local machine, unzip the just downloaded zip file stating_kit.zip and open R in the unziped strating_kit directory, (e.g. open strating_kit.Rmd with RStudio).

The unziped strating-kit directory contains:

  • A data.rds file containing the data.
  • A scoring program folder containing the program to compute the scoring (for you information).
  • A starting_kit.Rmd corresponding to the vignette of the Challenge (all useful information can be found here).
  • A submission_script.Rmd to modify and to use to submit your predictions.

[3] In the R console launch the following command:

rmarkdown::render("starting_kit.Rmd")

How to submit?

Now, let’s submit your prediction (zip file) in the Participate tab of the codalab challenge.

How is the scoring metric computed?

The discriminating metric will be computed on the A matrix: mean absolute error between the estimate and the groundtruth.

Download Size (mb) Phase
Starting Kit 44.163 #1 Exploration

Exploration

Start: July 22, 2019, midnight

Competition Ends

Aug. 23, 2019, 2 p.m.

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