Search found 3 matches

by liyangum
Thu Jun 17, 2021 2:30 pm
Forum: Main Forum
Topic: I have some questions about ResPRE
Replies: 1
Views: 131

Re: I have some questions about ResPRE

We did see the existence of imbalanced positive and negative samples. But we do not think that it is a problem.
Of course, you can set larger weights or other regular settings to try to make it more balance during the training.
by liyangum
Wed May 26, 2021 7:00 am
Forum: Main Forum
Topic: I have some questions about ResPRE
Replies: 5
Views: 431

Re: I have some questions about ResPRE

We used supervised machine learning to train ResPRE models for contact map predictioon. The supervised information should be the contact maps (binary matrix, 1 for being in contact) from pdb structures.
by liyangum
Sun May 23, 2021 8:25 pm
Forum: Main Forum
Topic: I have some questions about the formula in the ResPRE paper
Replies: 2
Views: 344

Re: I have some questions about the formula in the ResPRE paper

The calculation of frequencies with pseudo count has been used in many papers for coevolution analysis. For example, Eq 21 in plmDCA (https://arxiv.org/pdf/1211.1281.pdf), and Eq 1 in DCA paper (https://www.pnas.org/content/108/49/e1293).