Daniel Himmelstein
Head of Data Integration at Related Sciences. Digital craftsman of the biodata revolution.
Slides online at: slides.com
/dhimmel
/launch
Wednesday October 11, 2017
6:00–9:00 pm, Milkboy Philly
cognition
+
carcinoma
putting machine learning in the hands of cancer biologists
Cognoma Motto 1
The Cancer Genome Atlas
$425,000,000 project funded by the U.S. Government
33 types of cancer
- esophageal carcinoma
- glioblastoma multiforme
- head & neck squamous cell carcinoma
- kidney chromophobe
- kidney clear cell carcinoma
- kidney papillary cell carcinoma
- acute myeloid leukemia
- brain lower grade glioma
- liver hepatocellular carcinoma
- lung adenocarcinoma
- lung squamous cell carcinoma
- mesothelioma
- ovarian serous cystadenocarcinoma
- pancreatic adenocarcinoma
- pheochromocytoma & paraganglioma
- prostate adenocarcinoma
- rectum adenocarcinoma
- sarcoma
- skin cutaneous melanoma
- stomach adenocarcinoma
- testicular germ cell tumor
- thyroid carcinoma
- thymoma
- uterine corpus endometrioid carcinoma
- uterine carcinosarcoma
- uveal melanoma
machine learning
Predicting cancer mutations from gene expression
Using public domain TCGA data
(from Xena Browser)
7,306 samples
20,468 genes with expression
RNA-Seq
21,960 genes with mutation.
Sequencing
covariates
elastic net logistic regression
Precision Oncology
"the science of ensuring that a patient's treatment is specifically designed and targeted for their unique form of cancer"
everyone learns something new
Cognoma Motto 2
Tonight makes 27!
Pull requests model for contribution
Contribution per user by GitHub repository
35+ contributors
Childhood Cancer Data Lab
- Cancer Data: Claire McLeod (@clairemcleod)
- Machine Learning: Patrick Miller (@patrick-miller), Ryan Velazquez (@rdvelazquez), Jesse Prestwood-Taylor (@jessept), Yichuan Liu (@yl565)
- Backend: Derek Goss (@dcgoss), Andrew Madonna (@awm33), Kurt Wheeler (@kurtwheeler)
- Frontend: Benjamin Dolly (@bdolly)
- Community: Karin Wolok (@KarinSpiderwoman)
- Wildcards: Daniel Himmelstein (@dhimmel), Gregory Way (@gwaygenomics), Casey Greene (@cgreene)
Maintainers
still accepting contributions
Thanks!
Cognoma Launch Party
By Daniel Himmelstein
Cognoma Launch Party
Slides for the Cognoma Launch Party on October 11, 2017 at MilkBoy Philadelphia. Meetup info at https://meetu.ps/3dzlvc. Pictures from this event at https://photos.app.goo.gl/PdyIPjzYBfx91vty1.
