Before submitting my predictions paper, I spotted a paper with alternative methods for the same predictions. It appeared two weeks ago online-first in the same journal I'm submitting to.
Digging into it, I found several issues. To validate predictions, the authors cherry-picked empirical results from the same table of another paper. The results' type and time period, clear from the table, were not the ones assumed for the predictions, which essentially invalidates comparison. The paper's code is on GitHub, but not the scripts for input filtering; so no reproducing the results. The model stated in the paper is commented out, and the one in the code is trained on both training and validation sets, contrary to practice and the paper. If assessed fairly, the predictions would be rather less impressive. And it is hard to tell how they were actually obtained.
Q1: What should I do about these issues?
There are similar questions, such as 1, 2, 3, 4, 5, 6. However, the usual answers --- to move softly and slowly, or just park it --- is probably not the way to go: a flawed paper on public health in a major journal can have consequences. I've doubts about emailing the authors as I'm not sure how honest their mistakes were and why they would respond. (Surely, authors would triple-check this type of papers? Literally, "we publish; you perish".) I guess I could open code-related issues on GitHub, and see whether the authors engage. At least people using their code might take notice.
Q2: How should I proceed with the submission?
This journal is the best place for this research, and for many reasons I'd like to submit as soon as possible. The reviewers would probably request me to compare predictions with that paper's, which is fair, but not in the circumstances. Shall I just submit without mentioning the other paper? Or should I attach a diplomatic letter describing the issues? I don't think the original reviewers are at fault: the issues are hard to spot without manually cross-checking numbers and references and digging into the code base. Still, would it be wise to make some requests, so that my paper be reviewed fairly?