Deep Learning

In the last two months, a couple of groups have published papers applying deep learning to problems related to gene regulation:  protein-nucleic acid binding specificity [1] and chromatin state [2]. We will be talking about these soon.

Before discussing these papers, we think it will be useful to give people some time to get familiar with the fundamentals of artificial neural networks and deep learning. So, this coming *Monday* at our new time of 12 noon, we’ll have a meeting to talk about deep learning and work through each other’s questions. Beforehand, please check out some of the following resources and bring questions (or expertise you’d like to share!).

At the meeting, we’ll walk through the topics in this Nature review: http://www.nature.com/nature/journal/v521/n7553/full/nature14539.html

More resources:

Lecture slides from Mark’s machine learning class:  https://www.biostat.wisc.edu/~craven/cs760/lectures/ANNs-1.pdf, ANNs-2.pdf

Intro to neural networks from a programming perspective (just skimmed this one; looks like an interesting presentation):  http://karpathy.github.io/neuralnets/

[1] DeepBind (Alipanahi et al, Nature Biotech 2015)
http://www.nature.com/nbt/journal/v33/n8/full/nbt.3300.html
[2] DeepSEA (Zhou & Troyanskaya, Nature Methods 2015)
http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.3547.html