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R in Grenoble DATA CHALLENGES
Magali Richard & Florent Chuffart
Introduct ction Data challenges in class Data challenges for scientists Tutorial
CIT-SAB MEETING 2
R in Grenoble DATA CHALLENGES Magali Richard & Florent Chuffart - - PowerPoint PPT Presentation
R in Grenoble DATA CHALLENGES Magali Richard & Florent Chuffart - - PowerPoint PPT Presentation
R in Grenoble DATA CHALLENGES Magali Richard & Florent Chuffart Introduct ction Data challenges in class Data challenges for scientists Tutorial CIT-SAB MEETING 2 What is a data challenge? Ellrott et al. Genome Biology (2019) 20:195
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What is a data challenge?
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Ellrott et al. Genome Biology (2019) 20:195
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The challenge platform
Ø Enables participants to submit their codes Ø Automatically rank the participants
Alexis Arnaud CIT-SAB MEETING 12
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2013: Medical data. Result submission. COMPETITION BUNDLES 2014: Computer vision, speech, NLP, IR. MSCOCO: 361 participants. 2015: CODE SUBMISSION AutoML: 687 participants
- Hackathons. Coopetitions.
2016: ChaLab Wizard. USE IN EDUCATION 2017: 480 challenges, 10000 users. SCALABILITY, REUSABILITY, DYNAMIC COMPETITIONS See.4c: EU prize, 2 million Euros
History
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Introduction Data ch challenges in cl class Data challenges for scientists Tutorial
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A novel pedagogic approache
As practical work As homework As final evaluation
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Chagrade: a dedicated tool in codalab
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Introduction Data challenges in class Data ch challenges for sci cientists Tutorial
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Goal of our data challenge
- Quantification of tumor heterogeneity
CIT-SAB MEETING 3 Tumor cells Immune cells Normal cells CAF ?
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A challenge for scientists
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2 editions of the data challenge
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1rst edition (2018) 2nd edition (2019)
- Methylation Data
- One cancer type
- Cell lines
- Methylation and transcriptomic Data
- Several cancer types
- Primary tumors / cell lines
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When and where?
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- When: 25-29 of November 2019
- Where: Aussois (CAES CNRS), French Alps
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About the participants (n=34)
CIT-SAB MEETING 7 Engineers Graduate students Industry Postdoc Researchers Undergrad students Bioinformatics Computer science Data science Medical science Statistics Byelorussia France Germany Luxembourg Norway Sweden
Institut Curie UGA Grenoble CRC Cordeliers INSERM CEA Innate Pharma Verteego …
10 teams of 3-4 people
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Agenda
CIT-SAB MEETING 9 PRACTICALS
Talks
#1 #1 #2 #2 #2 #2
Feed Back Brain Storming
Guidelines
Social event Poster session
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Valorization of the first edition
Ø R package medepir
https://rdrr.io/github/bcm- uga/medepir/man/medepir-package.html
Ø Guidelines
Health data challenges organization: feedback, comments and recommendations.
Authors: Elise Amblard, Yuna Blum, Jane Merlevede, Magali Richard In preparation
In review in BCM bioinformatics
Ø Article Ø Blog posts
M Richard, C Decamps , F Privé, M Blum CIT-SAB MEETING 16
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From data challenges to benchmarks
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Introduction Data challenges in class Data challenges for scientists Tu Tutorial
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On line tutorial by Alexis Arnaud
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It’s up to you now!
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Thank you for your attention !
CIT-SAB MEETING 20
https://app.secure.griffith.edu.au/events/event/61593