Does a low score in mathematics on transcripts affect graduate admissions? (CS PhD USA) Background: CS Undergrad Applying to CS PhD Programs in the USA.
I have a GPA of 8.9 ~ (after converting) 3.5? (Not too sure, I am in a Tier-II College in India).
According to me, I feel a GPA of 8.9 isn't too bad, I guess I'm in the 87-93 percentile of my department. But my lowest scores are in 4 out of my 5 math papers. I only scored the best grade in my 5th semester.
2 A's, 1 B, 1 A, 1 O (Hierarchy of Grades: O A+ A B B+ C .. F)
I know CS PhD admit panels require mathematically sound students and I actually am quite good at math. The few preprints and publications I have are all in mathematically involved topics. They are primarily machine learning but quite a bit of math is involved. It is pure coincidence that I actually somehow managed to perform bad specifically in the math papers.
I have good grades in my computer science subjects, good SOPs and LORs (at least I think I do, they will be research dense), internships.
Question:

Does this really affect my chances of getting into a good program?
Is there any way I can offset this?
Does a good GRE Quant score help in this? (Don't mind my asking)

Extra Question: Should I opt for a master's, get good grades in the math subjects there and better my transcripts?
(I really want to start a PhD and skip my masters. I enjoy research a lot).
Sorry for so many questions, I really need some clarity.
I am also aware Machine learning is mostly math, what I meant to say was that the papers are not only code heavy but also contain good theory.
In the US a doctoral application is based on a variety of things, including GPA and individual course grades in a major field of study. But letters of recommendation are much more important here than in some other places. They need to be from people who know you well and will attest to the high probability of your success.
You also need a good Statement of Purpose, stating your short and longer term goals and how you are prepared to achieve them.
But getting a MS in the US is probably not going to be an advantage for you since it is unlikely to come with any funding, though doctoral study (as a TA) normally does.
My advice would be to apply to several universities for doctoral programs. Make the search fairly broad, not just concentrated in the top ranked schools. But the admission committees will look at everything and some good things might help to overcome some other not as good things.