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

Maintainers

still accepting contributions

Thanks!