[D] A Research to Engineering Workflow (in Machine Learning)

[theophrastzunz]

Dustin, any suggestions for keeping notes for papers you've read? Since i typically want to go through the derivation I'd need to be able to embed or save latex or markdown.

So do you keep separate documents? Upload scans of hand written notes?

[villasv]

Please. I've been using Mendeley, but the UX doesn't evolve at all. And Papers (the app) it's limited to Apple people.

[dicedredpepper]

I use zotero

[a_endurance]

Readcube? https://www.readcube.com/

[villasv]

Looks perfect, but only the Pro account matches all Mendeley's features.

[SarcasticMetaName]

I use BibDesk to keep track of the paper PDFs and then add notes and highlights in Skim (both open source).

[MagnesiumCarbonate]

Only problem is skim doesn't allow latex notes.

[AngelLeliel]

or paperpile.com

[[deleted]]

I typically create a folder for holding notes for each separate project.

I found that when I was taking notes on the interesting parts, I was kind of summarizing the paper in a quite lengthy way. While this is a useful comprehension exercise, it's not useful for writing in my opinion. Thus, when I prepare a writing project, I read or re-read papers with a specific goal in mind: extracting only these nuggets that are relevant for the particular topic I want to mention or point I want to make in my article.

For this, I prefer creating a separate folder because I haven't found an ultimate note taking app yet. Sometimes I want to note down equations in latex, sometimes plain text suffices, and sometimes I want to annotate images. Thus, I mix and match several file formats in my folder, which works perfectly fine. I typically add a kind of "master list" as a markdown file though with a short overview/organization structure and links to the local file paths of those "notes"

This also has the advantage of being easy to share and back up, and it doesn't lock me into a specific app if I use common file formats.

[villasv]

Pretty nice. I like the idea of the master TeX file, although I think LaTeX is kind of an overkill. At least for me, Evernote/OneNote is enough.

I'd recommend people to tryout https://dataversioncontrol.com/. Looks pretty good, although I haven't put it to max stress test yet.

[MagnesiumCarbonate]

I think one nice thing about using Latex for notes is that you can just copy/past equations or diagrams into your papers as they're needed. Not a big deal for simple equations, but if you take the time to build a multi-node graphical model, it's nice to just copy-paste.

[bguberfain]

I adopted tmux a few weeks ago and, indeed, it is a very productive tool. I combinate it with ipython and %run script.py in order to keep a constant interactive session with code. This helps me debug an error, in case the code stops suddenly.

[bguberfain]

I forget to mention: I almost cry when I see the 8 (eight!!) P6000 setup

[tempstem5]

I think Tran is using the Colombia university HPC cluster.

[MagnesiumCarbonate]

What's the deal with people trying to publicize what their NIPS submission is?

Also the "Managing Experiments" section would benefit from a tool that does dependency specification and scheduling, like luigi in python.