Penguin is all about web spamming. In my view first you should remove your spam links. If spma links like article and directory van not be removed, then you can directly remove it by a tool of Google in Google webmaster i.e. https://www.google.com/webmasters/tools/disavow-links-main
You also find more tips from this blog. Please read it.
http://www.zealousweb.net/blog/factors-associated-with-the-google-penguin-update/
