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cwalker4 / deepiv-gwas

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Are CNNs useful for our data? #7

Closed cwalker4 closed 6 years ago

cwalker4 commented 6 years ago

Some preliminary reading:

https://www.quora.com/How-can-convolutional-neural-networks-be-used-for-non-image-data

https://www.quora.com/Are-convolutional-neural-networks-useful-only-for-image-recognition-or-applications-having-spatial-features

My best guess based on skimming those links: yes, if our input data is something like a full genome where entries that are close together in our vector are also physically close to one another on the chromosome.

billyferguson commented 6 years ago

Not sure how useful this is for our data since I don't know all the bio. But this seems useful.

https://academic.oup.com/bioinformatics/article/32/12/i121/2240609

billyferguson commented 6 years ago

Here's a running list of deep learning applications in Bio (specifically in Genomics)

https://github.com/hussius/deeplearning-biology

cwalker4 commented 6 years ago

Here are some lecture slides on CNNs for genomics from CS273B. Our project advisor took this class, so it might be good to have a conversation with him about how we should be thinking about CNNs and whether we should consider using them.

Anshul-Lecture3-slides.pdf

Lecture2Slides-ConvNetsFuncGenomics.pdf

cwalker4 commented 6 years ago

no.