DL and Genomics


(Akhil Rajput) #1

Hi,

Could DL be employed to analyze Genomics data, the data which is much much wider (1 Million to 30 Million columns) than long (10 K to 100 K rows)? Any suggestions, resources, examples will be highly appreciated.

Thanks


(Jeremy Howard) #2

Here’s a recent review paper:

https://arxiv.org/abs/1802.00810


(Akhil Rajput) #3

Awesome, I will go through the suggested review. Thanks


(Cedric Chee) #4

Hi. I have worked in the area on how to infer genomics information from MRI images and using it to predict cancer growth in patients in the Asia context. I am also currently self learning bioinformatics and applying it in genomics data in my side-projects.

I learned about deep learning in biology and medicine landscape through this paper “Opportunities and obstacles for deep learning in biology and medicine”. I think it is quite useful.

I also followed the work of:

RNN/NLP in genomics:

  • Finding functional regions (e.g., regulatory regions)
  • DeepGo (protein function classification from sequence)

If you are looking for the cutting edge model zoo for regulatory genomics including Google DeepVariant, check out:

This is not meant to be exhaustive. Almost impossible as there’s so much out there now. Here’s one giant list of deep learning implementations in biology. :roll_eyes:


(Akhil Rajput) #6

Thanks for the fantastic information.

What kind of DL - Genomics projects you are doing / have done? Any insight will be really helpful.

Thanks a lot