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What tools do you usually use to draw graphical models in research papers? I mostly use tikz, but it's sometimes a bit labor-intensive getting everything to come out right (and I've had reinstalls/upgrades of texlive/pgf break all the figures in a paper, which was annoying).

Some other options I can think of are Dia, Inkscape, graphviz, and Mathematica (but these last two might need a bit of hand holding)>

asked Sep 01 '10 at 18:57

Alexandre%20Passos's gravatar image

Alexandre Passos ♦
2554154278421

1

TpX is the one I have been using. It is not perfect, but it is simple for drawing graphical models.

(Sep 03 '10 at 15:29) Denzel

10 Answers:

I've always been a big fan of xfig. No fuss, but still everything you want in a schematic diagram drawing program. The UI is kind of old school, but whatever, it works.

answered Sep 02 '10 at 12:23

aditi's gravatar image

aditi
85072034

2

Agreed. The xfig UI seems archaic but it actually is really good. I can draw really quickly with it compared to Inkscape and Illustrator.

(Sep 03 '10 at 08:05) Noel Welsh

If you use Python, it is worth taking a look at networkX. In R, there is a complete set of packages for GMs, see the gR Task view.

Otherwise, check this website which provides a comprehensive list of available software.

answered Sep 03 '10 at 08:30

chl's gravatar image

chl
9138

On Mac OS, you can actually just use Keynote (the PowerPoint equivalent). Just draw on a slide. It works really well for me. You can export your drawing as PDF vector graphic. Just select and copy, open Preview, do "Insert from Clipboard" and save as PDF.

Of course, if your graph is too large to draw by hand or you need automatic layout, then graphviz is the better alterntive.

answered Sep 03 '10 at 12:34

Frank's gravatar image

Frank
1349274453

I found the TutorialGMLTX tutorial and template (which uses Latex) to be quite handy.

Note: One element that I required, which was not covered in the included tutorial, was a dotted arc/edge. For that, you can pass the "linestyle=dotted" option to psline, as described in this PSTricks documentation.

answered Apr 28 '11 at 19:24

Ken%20Dwyer's gravatar image

Ken Dwyer
711

I just heard of nodebox yesterday. http://nodebox.net/code/index.php/Home

It's free and supposed to be good.

answered Apr 28 '11 at 22:53

Aman's gravatar image

Aman
2614916

I usually use a combination of OmniGraffle (which uses graphviz under the hood) and LaTeXiT, a Mac application that creates transparent PDFs from LaTeX math markup. Then I get the full power of LaTeX for labeling the figure. I usually turn off the automatic shadows though (they usually look terrible in print).

answered May 14 '11 at 22:25

David%20Warde%20Farley's gravatar image

David Warde Farley ♦
551820

edited May 14 '11 at 22:25

If you're already comfortable with tikz, there are some good macros written by Laura Dietz. They allow template representations, generative models, directed models, factor graph notation, etc.

zip file
pdf with examples

answered Jul 26 '11 at 16:21

Brian%20Martin's gravatar image

Brian Martin
31123

I recommend IPE. It is like a modern version of xfig. It is multi-platform, you can write Latex code inside the diagrams, and you can save as EPS or PDF.

answered Jul 26 '11 at 17:36

Alejandro's gravatar image

Alejandro
301610

Try the pstricks package com.braju.graphicalmodels from http://www1.maths.lth.se/matstat/staff/hb/mypackages/

answered Feb 09 '12 at 14:15

Kevin%20Murphy's gravatar image

Kevin Murphy
161

Try the pstricks package com.braju.graphicalmodels from http://www1.maths.lth.se/matstat/staff/hb/mypackages/

answered Feb 09 '12 at 14:15

Kevin%20Murphy's gravatar image

Kevin Murphy
161

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