Posted by: cbouyio | 15 June, 2015

The network nonsense of Manolis Kellis

Bits of DNA

This is the second in a series of three posts (part1, part3) on two back-to-back papers published in Nature Biotechnology in August 2013:

  1. Baruch Barzel & Albert-László Barabási, Network link prediction by global silencing of indirect correlationsNature Biotechnology 31(8), 2013, p 720–725. doi:10.1038/nbt.2601
  2. Soheil Feizi, Daniel Marbach, Muriel Médard & Manolis Kellis, Network deconvolution as a general method to distinguish direct dependencies in networksNature Biotechnology 31(8), 2013, p 726–733. doi:10.1038/nbt.2635

The Barzel & Barabási paper we discussed in yesterday’s blog post is embarrassing for its math, shoddy “validations” and lack of results. However of the two papers above it is arguably the “better” one. That is because the paper by Soheil Feizi, Daniel Marbach, Muriel Médard & Manolis Kellis, in addition to having similar types of problems to the Barzel & Barabási paper, is also dishonest and fraudulent

View original post 3,337 more words

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Responses

  1. The story is quite fascinating as it unfolds at Lior Pachter blog, however there are three links which deserve some further mention here as they all address most of the questions the initial post has raised.

    A page from Manolis website with a collective attempt to answer most of Lior’s comments.
    http://compbio.mit.edu/nd/Response_to_Nonsense_Blog_Post.pdf

    The Nature Biotechnology “Corrigendum” of the initial paper.
    http://www.nature.com/nbt/journal/v33/n4/full/nbt0415-424.html

    and a video specifying how to reproduce the code and the results.
    http://compbio.mit.edu/nd/try_it_out.html

    I believe that all the story and the comments in Lior’s blog (some uninformative malice removed) as well as the detailed answers from Manolis are of great pedagogical value for any junior computational biologist!


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