As a female software engineer will my salary be less than my male counterparts if I have a master’s degree and relevant research experience?

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Probably.

I read about a study once that attributed the salary gap in most professions to willingness to negotiate. The gold standard of job negotiation is to have multiple offer letters that you can then play off each other. Actually doing this is really hard, but if you can bring yourself to conduct your job search in such a manner, you can dramatically increase what you end up with.

Another negotiation tactic to remember is that salary is only one dial. Focusing exclusively on that dial actually reduces your bargaining position. Vacation days, work from home days, signing bonus, equity, literally everything about your job can be up for grabs.

What I would like you to do is to dream up your perfect job, and write that down in the form of an offer letter. Then when they offer you a job, ask about each of those things one after the other. If you could get everything else but the salary you wanted, you could make out like a bandit anyway.

Salary is literally the most expensive form of compensation a company can offer you. I’m not saying this to tell you you should accept a lower one, I’m saying that if salary seems non-negotiable, that means the company needs to make their job more competitive in other ways.