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New Tip 1 #241

Merged
merged 23 commits into from
Oct 13, 2020
Merged

New Tip 1 #241

merged 23 commits into from
Oct 13, 2020

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Benjamin-Lee
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Did you add yourself as a contributor if this is your first contribution?

  • Yes, I added myself or am already a contributor

Any more details?

Per the discussion in #228, this PR moves the content in the current tip 1 around (only removing a few lines) and creates space for a new first tip focusing on whether you should use DL in the first place.

@cgreene
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cgreene commented Oct 7, 2020

I think this is going in a good direction. What are you thinking re: how to decide? For me it comes down to:

  • Do we expect that the features are not already heavily optimized for the task.
  • Are we ok with the features being combined in somewhat difficult to untangle ways to carry out the task?
  • Do we have one or more plausible strategies for dealing with the large number of parameters?
  • Does it matter that there are likely an arbitrary number of equivalent solutions?

It might come down to more things, but this is a bit off the cuff of how I'd think about things.

@Benjamin-Lee Benjamin-Lee marked this pull request as ready for review October 11, 2020 00:43
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Converting this from draft status to be ready for review.

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Benjamin-Lee commented Oct 11, 2020

BTW, this closes #228

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@chevrm chevrm left a comment

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New lines 3 & 4 still needs some work.

@Benjamin-Lee
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New lines 3 & 4 still needs some work.

What do you have in mind? I'm trying to get at the misleading conception that since NN are a universal function approximators they should be used universally.

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chevrm commented Oct 11, 2020

I think the sentiment works; just needs some tweaking of the language. Maybe something like

In recent years, the number of publications implementing DL in biology have risen tremendously.
Given DL's usefulness across a range of scientific questions and data modalities, it may appear that it is capable of anything.
Neural networks are universal function approximators, meaning that they are in principle capable of learning any function [@doi:10.1007/BF02551274; @tag:hornik-approximation].
If DL is so powerful and popular, why would one ever not choose to use it?

I still don't love the "it may appear that it is capable of anything" bit. Any suggestions?

@Benjamin-Lee
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I still don't love the "it may appear that it is capable of anything" bit. Any suggestions?

What about something like "a panacea for modeling problems"?

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chevrm commented Oct 11, 2020

I still don't love the "it may appear that it is capable of anything" bit. Any suggestions?

What about something like "a panacea for modeling problems"?

Yes, I think that works well

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Looks good in general! Some generally small comments here and there, a few of which may require a couple of extra sentences.

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@Benjamin-Lee
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@SiminaB thanks for the feedback. Going to bed now but will work on it tomorrow.

Projects such as Keras [@https://keras.io], a high-level interface for TensorFlow, make it relatively straightforward to design and test custom DL architectures.
In the future, projects such as these are likely to bring DL experimentation within reach to even more researchers.

There are some types of problems in which using DL is strongly indicated over ML.
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I think this part is missing "why" to synthesize the examples.

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Basically, what I'm getting at is that you don't need to start out with the most high powered tools there are now that there are more beginner-friendly ones that are stable. If you need a NN architecture that doesn't exist out of the box in one of the higher level tools but isn't so exotic that you need TensorFlow primitives, a tool like Keras might be a good middle ground.

@cgreene
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cgreene commented Oct 12, 2020

Of the presented options I think I prefer "Decide whether deep learning is appropriate for your problem"

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agitter commented Oct 12, 2020

I also like "Decide whether deep learning is appropriate for your problem". It suggests that you have a goal (problem) and want to consider appropriate tools, which may or may not be deep learning.

@Benjamin-Lee
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@cgreene and @agitter I've gone and renamed the tip. I think it sounds better also and is less negative than the other option

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I like the new tip. I've just made a few minor inline changes based on people's comments

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@Benjamin-Lee Benjamin-Lee linked an issue Oct 13, 2020 that may be closed by this pull request
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ttriche commented Oct 13, 2020 via email

Benjamin-Lee added a commit that referenced this pull request Oct 20, 2020
…in-tip-2

Remove a paragraph that was moved to tip 1 in #241
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