I've ported the NIPS 2016 template so that it can be used within LyX. You can download the template here: https://github.com/adefazio/nips-lyx-template. Only minimal changes were needed to the default LyX settings. I had to change the encoding and font settings to match the NIPS style since LyX's values conflicted with the preamble. If you have any issues with it, let me know.