From listmaster animalgenome.org Mon Jul 22 11:10:36 2019
Return-Path: <listmasteranimalgenome.org>
From: DANIEL GIANOLA <gianolaansci.wisc.edu>
Subject: Re: Guide on deep learning
Postmaster: submission approved by list moderator
To: Members of AnGenMap <angenmapanimalgenome.org>
Date: Mon, 22 Jul 2019 11:10:36 -0500
A DEEP THANK YOU, Miguel and Laura. Hopefully, we will all learn DEEPly,
and see if knowledge of the DEEP architecture of complex traits can ever
be learned.
We certainly cannot predict with the SHALLOW y=Xb+e (GWAS), and it is argued
that if the whole-genome is implicated, then GWAS is not informative (Tam et
al. 2019, Nat. Rev. Genetics). That line of reasoning implies that perhaps
we cannot learn much with the less shallow SHALLOW y=Xb+Zu+e--all loci get
implicated-- although predict we certainly can!
Maybe DEEP learning will implicate the whole-genome, the whole interactome,
the increasing army of DEEP phenotypes (images, sounds, odor--good and bad
ones, whatsapp, etc), and eventually, a DEEP MULTI-OMICS SINGLE STAGE BLUP
will become a focal topic in the next five years. Perhaps, Ignacy Misztal
will extend APY to DEEPY and Cheng-Fernando-Garrick will develop DEEP Bayes
Cpi-pipi-pipipi, etc. Here pi means first layer, pipi means the second layer,
and pipipipi stands for higher-dimensional stuff.
Another possibility is that we will drown in a DEEP sea of confusion, akin to
the situation of choosing a beer in a good Belgian brasserie or extracting a
meaningful message from the UN General Assembly.
Regards,
Daniel
________________________________
.From: miguel.perez <miguel.perezuab.es>
.Sent: Monday, July 22, 2019 8:02 AM
.To: Members of AnGenMap <angenmapanimalgenome.org>
.Subject: Guide on deep learning
Just in case you are wondering about how deep learning works, we have
posted an easy to follow script in github guide
https://github.com/...rezenciso/DLpipeline
and associated, somewhat more technical reference in
Genes, 10, 553.
https://www.mdpi.com/2073-4425/10/7/553
--
===============================================================
Miguel Perez-Enciso
ICREA professor
Centre for Research in Agricultural Genomics (CRAG)
and Facultat de Veterinaria UAB
Campus Universitat Autonoma Barcelona
Bellaterra
E-08193 Spain
Tel: +34 935636600 ext 3346
Fax: +34 935636601
miguel.perezuab.es
http://www.icrea.cat/...Enciso-255
http://bioinformatics.cragenomica.es/numgenomics/
http://scholar.google.es/...r=Lpl_-dcAAAAJ&hl=es
http://orcid.org/0000-0003-3524-995X
https://github.com/miguelperezenciso/
================================================================
|
