On what basis are you asserting that "The code in the paper does not have any copy restrictions or license"?
Without a license, published material falls under standard copyright law. In most countries, this means that all rights are reserved to the owner of the copyright (usually the author of the article or the publisher of the journal). While there are exceptions (which vary by country) that may permit legal usage of extracts, they're unlikely to extend so far as wholesale verbatim lifting of code.
(Even though the algorithm itself cannot be copyrighted, the particular expression in terms of choice of variable names, comments, code structure is subject to those laws)
So there is a fair chance that both you and the authors of the GPL modules you mention are violating the original author's copyright, unless they have genuinely released it under a permissive license. If they have done that, then redistributors can use whatever license they like.
As Dean Harding suggests in the comments below, a good place to start would be to contact the original authors of the paper to check the license on their code. If they're happy to explicitly provide it under a liberal license, both you and the GPL projects are likely to be fine (it is possible to violate the liberal licenses, but it's typically also fairly easy to remedy a breach even if you do make a mistake).
If you have the funds, another thing to do would be to find yourself a good copyright lawyer and ask them your licensing questions (preferably looking for one that understands open source licensing and can help with the tangled jurisdictional issues that can arise when making and distributing software online). Taking that action will count in your favour if you land in legal hot water further down the track. Note that I am not a lawyer, and even if I was, this still wouldn't be legal advice (since you wouldn't technically be my client).