deep-rules

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For full reproducibility, always report all details of your analyses, including sharing of data, methods, and models

4

hugoaerts

Understand the data

5

Before hitting the data with fancy DL algorithms, always spend some time to understand how the data were generated, how the samples are selected, and what were the assumptions in...

khyu

Have access to adequate infrastructure

4

**Have you checked the [list of proposed rules](https://github.com/Benjamin-Lee/deep-rules/issues?q=is%3Aissue+is%3Aopen+label%3Arule) to see if the rule has already been proposed?** - [x] Yes **Did you add yourself as a [contributor](https://github.com/Benjamin-Lee/deep-rules/blob/master/contributors.md) by making a...

rasbt

Close issues that have been addressed

16

If anyone wants to volunteer for this task, it'll definitely help clarify what still needs to be addressed in the manuscript. If no one is able to, I will get...

Benjamin-Lee

Discuss computational issues

1

Mention compute time issues, tools that are available, open source programming. The "Ten Quick Tips" for comp bio article linked in #1 specifically has "Program your software with open source...

SiminaB

New paper on DA for scRNA-seq

5

[Single-cell RNA-seq denoising using a deep count autoencoder](https://www.nature.com/articles/s41467-018-07931-2#ref-CR33) > **Denoising enables discovery of subtle cellular phenotypes** > After having evaluated DCA against competing methods, we tested if DCA denoising could...

tbrittoborges

Don't forget your ML fundamentals/Rules that apply to ML also apply to DL

2

**Have you checked the [list of proposed rules](https://github.com/Benjamin-Lee/deep-rules/issues?q=is%3Aissue+is%3Aopen+label%3Arule) to see if the rule has already been proposed?** - [x] Yes **Feel free to elaborate, rant, and/or ramble.** Maybe we could...

Benjamin-Lee

Make sure you are optimizing the right objective function!

3

**Have you checked the [list of proposed rules](https://github.com/Benjamin-Lee/deep-rules/issues?q=is%3Aissue+is%3Aopen+label%3Arule) to see if the rule has already been proposed?** - [x] Yes **Feel free to elaborate, rant, and/or ramble.** **Any citations for...

Isy89

Perform sanity checks and follow good coding practices

8

**Have you checked the [list of proposed rules](https://github.com/Benjamin-Lee/deep-rules/issues?q=is%3Aissue+is%3Aopen+label%3Arule) to see if the rule has already been proposed?** - [x] Yes **Did you add yourself as a [contributor](https://github.com/Benjamin-Lee/deep-rules/blob/master/contributors.md) by making a...

evancofer

Feature engineering is still (or is no longer) important

8

**Have you checked the [list of proposed rules](https://github.com/Benjamin-Lee/deep-rules/issues?q=is%3Aissue+is%3Aopen+label%3Arule) to see if the rule has already been proposed?** - [x] Yes **Did you add yourself as a [contributor](https://github.com/Benjamin-Lee/deep-rules/blob/master/contributors.md) by making a...

agitter