Hi, we're looking at using this package in some upcoming work so I'm just trying to understand the implementation a little better. Currently, I'm hung up on how you've implemented the hub-penalization as described in equation 2 of Akhmedov 2017.
p'_{v} = p_{v} - mu x degree(v)
From my understanding of the linked interpretation this is only penalizing the prizes of steiner nodes and not those given prizes, and conversely only the prize-nodes are scaled by b which isn't how I'd interpreted the equation in your manuscript.
Although, I see having just checked Forest's source code they do the same thing so I guess it was a misinterpretation on my behalf. Regardless, I can see value in prize-nodes being penalized by their degree as well. Is this something you ever considered doing or tested at all?
Hi, we're looking at using this package in some upcoming work so I'm just trying to understand the implementation a little better. Currently, I'm hung up on how you've implemented the hub-penalization as described in equation 2 of Akhmedov 2017.
p'_{v} = p_{v} - mu x degree(v)From my understanding of the linked interpretation this is only penalizing the prizes of steiner nodes and not those given prizes, and conversely only the prize-nodes are scaled by
bwhich isn't how I'd interpreted the equation in your manuscript.Although, I see having just checked Forest's source code they do the same thing so I guess it was a misinterpretation on my behalf. Regardless, I can see value in prize-nodes being penalized by their degree as well. Is this something you ever considered doing or tested at all?
Thanks, Sam
https://github.com/IOR-Bioinformatics/PCSF/blob/4e5f2707fdd096b760e5bb4ca60938a3c9836d78/R/PCSF.R#L127-L130