Rebuttal to the Letter to the Editor in response to the paper: proper evaluation of alignment-free network comparison methods
We rebut the allegations of Ali et al. (2016) that we mis-read their Ali et al. (2014) paper and that we carried out its flawed evaluation.
Alignment-free (AF) network comparison is used to quantify the level of similarity (or equivalently, distance) between input networks, irrespective of the node mapping between the networks. The need for improving AF measures arises from the computational intractability of the underlying subgraph isomorphism problem (Cook, 1971) and from the important applications that network comparison measures have in many domains, including computational biology. Alignment-based (AB) network comparisons directly account for the node mapping between the networks being compared, which AF measures do not.
An AF measure called NetDis was published in September 2014 by Ali et al. (2014). Unfortunately, Ali et al. (2014) did not properly evaluate NetDis: despite the focus of their study being the introduction of a new AF network distance measure, NetDis, they only evaluated NetDis against one outdated AB method and not against any of the existing AF measures. For example, RGFD (Pržulj et al., 2004) and GDDA (Pržulj, 2007) are AF measures that had been available for 10 and 7 years, respectively, before Ali et al. (2014) appeared. Another AF measure is GCD (Yaveroğlu et al., 2014), which was published 4 days after the NetDis paper was submitted, but over 5 months before NetDis was published. Hence, Ali et al. (2014) could certainly have compared NetDis to RGFD and GDDA. In addition, Ali et al. could also have compared NetDis to GCD in their letter to the Editor that we are rebutting here (Ali et al., 2016). It is unclear why Ali et al. (2014) decided not to provide such comparisons. For these reasons, Yaveroğlu et al. (2015) conducted an objective and comprehensive evaluation of the existing AF network distance measures, including RGFD, GDDA, GCD and NetDis, amongst others and showed that many of the claims of Ali et al. (2014) about NetDis were not supported by experimental evidence.