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<h1 id="applying-embeddings-to-dna-kmer-matching">Applying Embeddings to DNA KMer Matching</h1>
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Posted on Thu 22 June 2017 in <a href="http://pmlg.github.io/category/events.html">events</a>
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<p>This week we began with code from the fast.ai course in the beginners
session (6-7). In the advanced session (7-8) we listened to an actual
bio-informatics guru Phillipp Bayer talking about applying embeddings
to DNA kmer matching as inspired by Mike's talk last week.</p>
<p><a href="https://github.com/philippbayer/cats_dogs_redux/blob/master/Embeddings%20%2B%20keras.ipynb">Jupyter notebook from talk </a></p>
<p><a href="https://arxiv.org/abs/1701.06279 https://github.com/pnpnpn/dna2vec">The paper and code (the word2vec paper is also here)</a></p>
<p><a href="https://fivethirtyeight.com/features/dissecting-trumps-most-rabid-online-following/">This is the wonderful article on using arithmetic similar to word2vec to compare (hate-)subreddits</a>
(could be interesting to do this with DNA from different plants to see what falls out)</p>
<p><a href="https://rcc.uq.edu.au/flashlite">This is the high memory cluster</a>
You can apply for access if you have an Australian Access Federation (AAF) account, i.e., if you work for CSIRO or any Australian research institute.</p>
<p>Here in Perth there's <a href="https://www.pawsey.org.au/2016/09/applications-now-open-2017-access-to-pawsey-supercomputers/">Pawsey Centre</a>:
Looks like you need to be part of an Australian research institute as well to be eligible.</p>
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