Health Data Challenge (2nd edition): Matrix factorization and deconvolution methods to quantify tumor heterogeneity in cancer research

from November 25, 2019 to November 29, 2019

This interdisciplinary challenge will be dedicated to the quantification of intra-tumor heterogeneity using appropriate statistical methods on transcriptomic and methylation data.

Invited speakers

Michael Scherer from Max-Planck-Institut fur Informatik, Saarbrucken, Germany
Francisco Avila Cobos from Ghent University, Gand, Belgium
Jerome Cros from AP-HP, Paris, France


Scientific challenge

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 will be dedicated to the quantification of intra-tumor heterogeneity using appropriate statistical methods on (DNA) methylome and transcriptomic data in cancer.
In particular, it will focus on estimating cell types and proportion in biological samples (in vivo and in silico mixtures) for which transcriptome and/or methylome profiles have been generated.
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, …).
Participants will be made aware of several pitfalls when analyzing omics data (large datasets, missing data, different type of technologies/omics…).
This challenge will also be a unique opportunity to compare the performance of deconvolution methods between transcriptome and methylome data, which might have a great impact on clinical practice.
Participants will work in interdisciplinary teams.

Who can attend?

Undergrads, PhD students, postdoc, researchers, professors, clinicians and employees from the private sector are welcome.
We look for interdisciplinary expertise in biology, computer science, statistics, bioinformatics or medical sciences.
We expect that participants are familiar with R programming language (or equivalent) and with basic statistical notions. No prior knowledge in omics data is required.

Participants should bring their personal laptops.

General context

Health data challenge is part of a program dedicated to innovation in education. The aim of this program is to provide (i) analytical frameworks to bridge the gap between large dataset and personalized medicine in disease treatments and (ii) innovative pedagogical methods to train students and health professionals to big data analysis in health science. Integrating a large amount of data from different sources and using this knowledge to better characterize specificities of each individual will provide significant opportunities to improve disease diagnosis and to adapt accordingly patients’ treatment and care.


Monday November 25
Arrival of the participants
19h30-20h30 : Dinner
20h30-21h30 : Introduction to the Data Challenge
Tuesday November 26
09:00 to 09:45 : Invited speaker: J. Cros.
09:45 to 10:30 : Invited speaker: F. Avila Cobos
10:30 to 11:00 : Break
11:00 to 11:45 : Invited speaker: M. Scherer
11:45 to 12:30 : Introduction to challenge #1
12:30 to 14:00 : Lunch
14:00 to 16:00 : Challenge #1
16:00 to 16:30 : Break
17:00 to 18:30 : Challenge #1
18:30 to 20:00 : Poster session / Wine & Cheese
20:00 to 21:30 : Dinner
Wednesday November 27
09:00 to 10:00 : Debriefing on challenge #1
10:00 to 10:30 : Introduction to challenge #2
10:30 to 11:00 : Break
11:00 to 12:00 : Challenge #2
12:00 to 12:45 : Lunch
13:00 to 17:00 : Free time in the mountain
17:00 to 17:30 : Break
17:30 to 20:00 : Challenge #2
20:00 to 21:30 : Dinner (Grill-stone)
Thursday November 28
09:00 to 13:00 : Challenge #2
10:30 to 11:00 : Break
11:00 to 12:30 : Challenge #2
12:30 to 14:00 : Lunch
14:00 to 14:30 : Parallel sessions: Meeting report // Organize challenge in master cursus
19:30 to 20:00 : Announcement of the challenge #2 results
20:00 to 21:30 : Gala Dinner and cocktail party
Friday November 29
09:00 to 10:30 : Debriefing on challenge #2
10:30 to 11:00 : Break
11:00 to 12:00 : Challenge diffusion: How to organize your own health data challenge ?
12:00 to 13:30 : Lunch

Where and when

The challenge will take place during 5 days (November 25-29th, 2019) in Aussois, Vanoise, a charming small village in the Vanoise National Park (French Alps). It will end at 12pm on November 29th. If you want to leave Aussois after November 29th, you should spend the last night in another hotel nearby (e.g. hotel des mottets). The remote setting, along with the challenging program, were chosen to promote and enhance interactions between participants.

How to come


The closest airport is at Lyon Saint Exupery but you might also arrive in Paris. Then you should take the train from the airport to Modane. Check on the website of the SNCF for timetables and reservation.


The most convenient way to come to Aussois is to arrive by train at the railway station in Modane. Then, a bus shuttle will pick you up to go to the conference center (~15 minutes by bus). Please contact us if you need us to book the shuttle or if you want further information.
You can check timetables on the SNCF website.


There is a freeway to Modane, which is located at 15-20 minutes of the conference center in Aussois.
The tourist office provides additional information...


Registration fees include attendance to the courses, food, bus from the station, housing, conference banquet, and the social event on Wednesday. The challenge is limited to 48 participants.
Please register here
You will receive a validation of your submission and your registration will be studied on file.
You will receive a confirmation of your registration before October 10th.

•    Early birds (before June 30th) :  Students 150 € / Faculty-Postdoc 250 € / Industry 400 €
•    Normal (before September 12th) : Students 250 € / Faculty-Postdoc 450 € / Industry 600 €
•    A supplement of 50 euros will be charged if you prefer to stay in a single room rather than in a double room
Registration is free for the University of Grenoble Alpes' members.
How to pay:

•    By cash or credit card once you arrive at the conference center
•    By purchase order

Published on September 30, 2019

Practical informations