What to expect in ’18: science in the new year
https://www.Nature.com/articles/d41586-018-00009-5 Insights from cancer & ancient #genomes. Cures from #CRISPR. Progress in
#OpenAccess. Also, lots on outer space. But nothing on #cryoEM, #DeepLearning, #QuantumComputing or the brain connectome. HT @OBahcall
$GOOG Is Giving Away AI That Can Build Your Genome Seq. https://Research.GoogleBlog.com/2017/12/deepvariant-highly-accurate-genomes.html + https://www.Wired.com/story/google-is-giving-away-ai-that-can-build-your-genome-sequence GATK creators now doing a tensor-flow version. Release sounded a bit like IBM unveiling Deep Blue decades ago: “Today, we announce…DeepVariant, a #DeepLearning tech…"
Steven Salzberg’s response to deep variant:
https://www.forbes.com/sites/stevensalzberg/2017/12/11/no-googles-new-ai-cant-build-your-genome-sequence/#5953db7b5774
QT:{{"On Monday, Google released a tool called DeepVariant that uses deep learning—the machine learning technique that now dominates AI—to identify all the mutations that an individual inherits from their parents.1 Modeled loosely on the networks of neurons in the human brain, these massive mathematical models have learned how to do things like identify faces posted to your Facebook news feed, transcribe your inane requests to Siri, and even fight internet trolls. And now, engineers at Google Brain and Verily (Alphabet’s life sciences spin-off) have taught one to take raw sequencing data and line up the billions of As, Ts, Cs, and Gs that make you you.”
"}}
Google Is Giving Away AI That Can Build Your Genome Sequence
https://www.wired.com/story/google-is-giving-away-ai-that-can-build-your-genome-sequence/
The Serial-Killer Detector
https://www.NewYorker.com/magazine/2017/11/27/the-serial-killer-detector Journalist finds subtle yet predictive crime patterns with the computer. Wonder if #DeepLearning would be helpful here? Probably not // #CrimeMap
Qt:{{‘
A former journalist, equipped with an algorithm and the largest collection of murder records in the country, finds patterns in crime. “}}
New Theory Cracks Open the Black Box of #DeepLearning
https://www.QuantaMagazine.org/new-theory-cracks-open-the-black-box-of-deep-learning-20170921/ Highlights the importance of a compression phase for generalization
QT:{{”
“Then learning switches to the compression phase. The network starts to shed information about the input data, keeping track of only the strongest features — those correlations that are most relevant to the output label. This happens because, in each iteration of stochastic gradient descent, more or less accidental correlations in the training data tell the network to do different things, dialing the strengths of its neural connections up and down in a random walk. This
randomization is effectively the same as compressing the system’s representation of the input data. As an example”
“}}
an intuitive example of how CNN works
Zhou, J. and Troyanskaya, O.G. (2015). Predicting effects of noncoding variants with deep learning–based sequence model. Nature Methods, 12, 931–934.
Predicting (& prioritizing) effects of noncoding variants w. [DeepSEA] #DeepLearning…model
https://www.Nature.com/nmeth/journal/v12/n10/full/nmeth.3547.html Trained w #ENCODE data
The Great AI Awakening
http://www.NYTimes.com/2016/12/14/magazine/the-great-ai-awakening.html Quick history of #DeepLearning & its dramatic success in translation. Is med. diagnosis next?
Now flattered to have had 2 Hinton alumni in my lab…!
Basset: #DeepLearning the regulatory code w/…NNs by @noncodarnia lab http://genome.cshlp.org/content/early/2016/05/03/gr.200535.115 Has score for all possible SNVs in the genome
“Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks”
#Deeplearning framework for modeling…RBP sites
http://nar.oxfordjournals.org/content/44/4/e32 Uses topic models & determines key primary & tert. struct. features
$AAPL’s #DeepLearning Curve
http://www.bloomberg.com/news/articles/2015-10-29/apple-s-secrecy-hurts-its-ai-software-development A very secretive culture controlling Siri & your phone