There are several issues in play here -- the relatively new self-employment, the fact that you're a doctor, and the extraordinary startup costs. Being self-employed for three years is good, and meets the minimum requirement for many programs. If your business costs were higher in the first year or two, you'll be happy to know that many programs, including Fannie Mae, only require one year of taxes. So if your most recent return shows good income, you're okay.
The next thing to consider is how underwriters look at income.
Your accountant can easily work this out with a Fannie Mae Form 1084, Cash Flow Analysis. Some items, like depreciation, get added back into your taxable income. As do extraordinary expenses. Others, like windfall income, may be removed from qualifying income.
From there, our Home Affordability calculator https://themortgagereports.com/mortgage-affordability-calculator
can help you see what you can comfortably afford.
Finally, there are special programs out there for doctors (because your income is known to be increasing and stable), which may work if a traditional loan doesn't. These can cost more.
And for all self-employed applicants whose tax returns don't affect their cash flow, there are bank statement loans, and your income is established by a 24 month average of deposits running through your accounts, not your taxable income. Again, these tend to cost more than traditional mortgages.