Your good background to be admitted into CS PhD program

Synopsis: Your grades in undergraduate or master is important, but the most crucial is your ability to do high-quality independent research.

Question: What are my chances for getting into a top CS PhD program (Like Harvard, Columbia, NYU, etc.) with a MS in CS, 2 accepted IEEE conf. papers, 2 years of research exp. in deep learning on neuroscience datasets, 162 quant 154 verbal GRE, and a 3.7 GPA?

You’d better have some strong research results. At least in computer science, PhD applicants with graduate-school experience are held to a higher standard than PhD applicants without graduate-school experience. Applying with a master’s degree means you’re competing with lots of other applicants with masters degrees and strong publication records. That makes publishable (if not published) high-quality research a de facto admission requirement for you. (Publications are not a de facto PhD admission requirement for applicants without graduate-school experience. They certainly help, but lots of PhD students are admitted without them. Even at top departments. Even in machine learning.)

Okay, good, you have publications. But are they actually good? I’m not just asking whether they’re published in good conferences—although even that is not guaranteed by having a recognized publisher, no matter who that publisher is. (IEEE in particular has been known to sponsor some really sketchy conferences.) I’m asking whether the research itself is novel, interesting, creative, timely, well-motivated, well-written, likely to have long-term impact, and recognized as all of the above by experts in the field?
 

Just as importantly: Did you personally make a strong intellectual contribution to those papers? Can you describe both your specific contribution and your related future research plans, using the idiomatic language of successful researchers in your target field? Do you have strong recommendation letters from visible researchers in your field, who can speak directly to the high quality of your research, and in particular of your specific contributions to that research?

In short, can you provide concrete, compelling evidence of your potential for high-quality independent research?
 

Assuming this is your undergrad GPA, this is high enough that the admissions committee will actually look at your application, but that’s all it means. If this is your graduate-school GPA, it’s high enough not to be a red flag, but that’s it.
 

Finally, you don’t even mention whether there are faculty at “Harvard, Columbia, NYU, etc.” whose research interests align with your own. If there are, you might have a shot. If there aren’t (or if the faculty you’d like to work with in those departments aren’t taking new PhD students) then your chances are much much worse—fortunately for you. The last thing you want to do is go to a PhD program where none of the faculty wants to work with you.